1
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Saito S, Arai MA. Methodology for awakening the potential secondary metabolic capacity in actinomycetes. Beilstein J Org Chem 2024; 20:753-766. [PMID: 38633912 PMCID: PMC11022428 DOI: 10.3762/bjoc.20.69] [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: 12/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.
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Affiliation(s)
- Shun Saito
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Midori A Arai
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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2
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Augustijn HE, Roseboom AM, Medema MH, van Wezel GP. Harnessing regulatory networks in Actinobacteria for natural product discovery. J Ind Microbiol Biotechnol 2024; 51:kuae011. [PMID: 38569653 PMCID: PMC10996143 DOI: 10.1093/jimb/kuae011] [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: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches. ONE-SENTENCE SUMMARY This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Anna M Roseboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, The Netherlands
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3
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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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4
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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 UniversityCairoEgypt
| | - Marwa H. A. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef UniversityBeni-Suef 62511Egypt
| | - Ahmed O. Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit UniversitySohag 82511Egypt
| | - 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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5
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Ibrahimi M, Loqman S, Jemo M, Hafidi M, Lemee L, Ouhdouch Y. The potential of facultative predatory Actinomycetota spp. and prospects in agricultural sustainability. Front Microbiol 2023; 13:1081815. [PMID: 36762097 PMCID: PMC9905845 DOI: 10.3389/fmicb.2022.1081815] [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: 10/27/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
Actinomycetota in the phylum of bacteria has been explored extensively as a source of antibiotics and secondary metabolites. In addition to acting as plant growth-promoting agents, they also possess the potential to control various plant pathogens; however, there are limited studies that report the facultative predatory ability of Actinomycetota spp. Furthermore, the mechanisms that underline predation are poorly understood. We assessed the diversity of strategies employed by predatory bacteria to attack and subsequently induce the cell lysing of their prey. We revisited the diversity and abundance of secondary metabolite molecules linked to the different predation strategies by bacteria species. We analyzed the pros and cons of the distinctive predation mechanisms and explored their potential for the development of new biocontrol agents. The facultative predatory behaviors diverge from group attack "wolfpack," cell-to-cell proximity "epibiotic," periplasmic penetration, and endobiotic invasion to degrade host-cellular content. The epibiotic represents the dominant facultative mode of predation, irrespective of the habitat origins. The wolfpack is the second-used approach among the Actinomycetota harboring predatory traits. The secondary molecules as chemical weapons engaged in the respective attacks were reviewed. We finally explored the use of predatory Actinomycetota as a new cost-effective and sustainable biocontrol agent against plant pathogens.
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Affiliation(s)
- Manar Ibrahimi
- Laboratory of Molecular Chemistry, Materials and Catalysis, Faculty of Sciences and Technics, Sultan Moulay Slimane University, Beni-Mellal, Morocco,Higher School of Technology Fkih Ben Salah, Sultan Moulay Slimane University, Fkih Ben Salah, Morocco
| | - Souad Loqman
- Laboratory of Microbiology and Virology, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Marrakesh, Morocco
| | - Martin Jemo
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Mohamed Hafidi
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco
| | - Laurent Lemee
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP–CNRS UMR 7285), Université de Poitiers, Poitiers, France
| | - Yedir Ouhdouch
- AgroBiosciences Program, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco,Labelled Research Unit N°4 CNRST, Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakesh, Morocco,*Correspondence: Yedir Ouhdouch,
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7
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Yanagisawa M, Asamizu S, Satoh K, Oono Y, Onaka H. Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020. PLoS One 2022; 17:e0270379. [PMID: 35834474 PMCID: PMC9282665 DOI: 10.1371/journal.pone.0270379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022] Open
Abstract
Streptomyces lividans TK23 interacts with mycolic acid-containing bacteria (MACB), such as Tsukamurella pulmonis TP-B0596, and this direct cell contact activates its secondary metabolism (e.g., the production of undecylprodigiosin: RED). Here, we employed carbon (12C5+) ion beam-induced mutagenesis to investigate the signature of induced point mutations and further identify the gene(s) responsible for the production of secondary metabolites induced by T. pulmonis. We irradiated spores of the Streptomyces coelicolor strain JCM4020 with carbon ions to generate a mutant library. We screened the RED production-deficient mutants of S. coelicolor by mixing them with T. pulmonis TP-B0596 on agar plates, identifying the red/white phenotype of the growing colonies. Through this process, we selected 59 RED-deficient mutants from around 152,000 tested spores. We resequenced the genomes of 16 mutants and identified 44 point mutations, which revealed the signatures induced by 12C5+-irradiation. Via gene complementation experiments, we also revealed that two genes-glutamate synthase (gltB) and elongation factor G (fusA)-are responsible for the reduced production of RED.
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Affiliation(s)
- Masaomi Yanagisawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
| | - Katsuya Satoh
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Yutaka Oono
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, Quantum Beam Science Research Directorate, National Institutes for Quantum Science and Technology, Takasaki, Gunma, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
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8
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Kato M, Asamizu S, Onaka H. Intimate relationships among actinomycetes and mycolic acid-containing bacteria. Sci Rep 2022; 12:7222. [PMID: 35508597 PMCID: PMC9068768 DOI: 10.1038/s41598-022-11406-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 01/07/2023] Open
Abstract
Co-culture is an efficient strategy for natural product discovery. We have used mycolic acid-containing bacteria (MACB) Tsukamurella pumonis TP-B0596 to induce secondary metabolism by actinomycetes and have found several natural products. We also observed that MACB attached to the mycelium of Streptomyces lividans forming coaggregates during combined-culture. This stimulated interest in the interactions among actinomycetes and MACB, and we found that soil isolated cultures contained a mixture of actinomycetes and MACB. Our previously observed interactions were the result of selective screening and combination of bacteria in the lab, which warranted investigation of the existence of these interactions in the natural soil environment. Therefore, in this paper, we report the interaction between a co-isolated natural pair of actinomycetes and MACB in terms of morphology and metabolic changes. A natural pair of actinomycetes and MACB co-aggregated in liquid culture and showed metabolic changes. Interestingly, co-aggregated actinomycetes and MACB were re-isolated from soil with no obvious morphological colony differences from the colony of a single strain. The results demonstrate that there is a stochastic chance of picking colonies containing co-aggregated actinomycetes and MACB, which suggests that the pair can exist in co-aggregate form in the soil environment and interact with each other.
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Affiliation(s)
- Manami Kato
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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9
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Oku N, Takemura S, Onaka H, Igarashi Y. NMR characterization of streptogramin B and L-156,587, a non-synergistic pair of the streptogramin family antibiotic complexes produced inductively by a combined culture of Streptomyces albogriseolus and Tsukamurella pulmonis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:261-270. [PMID: 34547830 DOI: 10.1002/mrc.5219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The complete 1 H and 13 C NMR characterization of streptogramin B (1), the major component of a clinically important synergistic antibiotic complex, was presented for the first time, along with those of L-156,587 (2), a dehydrated congener of streptogramin A (3). Compounds 1 and 2 were not synergistic and produced by Streptomyces albogriseolus in co-culture with Tsukamurella pulmonis, which poses a question on the adaptive significance of the induced production of this antibiotic pair.
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Affiliation(s)
- Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Shion Takemura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Hiroyasu Onaka
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
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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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Ossai J, Khatabi B, Nybo SE, Kharel MK. Renewed interests in the discovery of bioactive actinomycete metabolites driven by emerging technologies. J Appl Microbiol 2022; 132:59-77. [PMID: 34265147 PMCID: PMC8714619 DOI: 10.1111/jam.15225] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 01/03/2023]
Abstract
Actinomycetes are prolific sources of bioactive molecules. Traditional workflows including bacterial isolation, fermentation, metabolite identification and structure elucidation have resulted in high rates of natural product rediscovery in recent years. Recent advancements in multi-omics techniques have uncovered cryptic gene clusters within the genomes of actinomycetes, potentially introducing vast resources for the investigation of bioactive molecules. While developments in culture techniques have allowed for the fermentation of difficult-to-culture actinomycetes, high-throughput metabolite screening has offered plenary tools to accelerate hits discovery. A variety of new bioactive molecules have been isolated from actinomycetes of unique environmental origins, such as endophytic and symbiotic actinomycetes. Synthetic biology and genome mining have also emerged as new frontiers for the discovery of bioactive molecules. This review covers the highlights of recent developments in actinomycete-derived natural product drug discovery.
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Affiliation(s)
- Jenifer Ossai
- University of Maryland Eastern Shore, School of Agriculture and Natural Sciences, One Backbone Road, Princess Anne, MD 21853, USA
| | - Behnam Khatabi
- University of Maryland Eastern Shore, School of Agriculture and Natural Sciences, One Backbone Road, Princess Anne, MD 21853, USA
| | - S. Eric Nybo
- Ferris State University, College of Pharmacy, Big Rapids, Michigan, USA
| | - Madan K. Kharel
- University of Maryland Eastern Shore, School of Pharmacy and Health Professions, Department of Pharmaceutical Sciences, One Backbone Road, Princess Anne, MD 21853, USA,Corresponding author:
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12
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Zong G, Fu J, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. Use of elicitors to enhance or activate the antibiotic production in streptomyces. Crit Rev Biotechnol 2021; 42:1260-1283. [PMID: 34706600 DOI: 10.1080/07388551.2021.1987856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Streptomyces is the largest and most significant genus of Actinobacteria, comprising 961 species. These Gram-positive bacteria produce many versatile and important bioactive compounds; of these, antibiotics, specifically the enhancement or activation of their production, have received extensive research attention. Recently, various biotic and abiotic elicitors have been reported to modify the antibiotic metabolism of Streptomyces, which promotes the production of new antibiotics and bioactive metabolites for improvement in the yields of endogenous products. However, some elicitors that obviously contribute to secondary metabolite production have not yet received sufficient attention. In this study, we have reviewed the functions and mechanisms of chemicals, novel microbial metabolic elicitors, microbial interactions, enzymes, enzyme inhibitors, environmental factors, and novel combination methods regarding antibiotic production in Streptomyces. This review has aimed to identify potentially valuable elicitors for stimulating the production of latent antibiotics or enhancing the synthesis of subsistent antibiotics in Streptomyces. Future applications and challenges in the discovery of new antibiotics and enhancement of existing antibiotic production using elicitors are discussed.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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13
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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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14
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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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15
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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: 41] [Impact Index Per Article: 13.7] [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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16
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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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17
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Pan C, Kuranaga T, Cao X, Suzuki T, Dohmae N, Shinzato N, Onaka H, Kakeya H. Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis. J Org Chem 2021; 86:1843-1849. [PMID: 33410699 DOI: 10.1021/acs.joc.0c02660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.
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Affiliation(s)
- Chengqian Pan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Takefumi Kuranaga
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Xun Cao
- Ocean College, Zhejiang University, Hangzhou 310058, China
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Bioscience Building, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences & Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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18
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Alkayyali T, Pope E, Wheatley SK, Cartmell C, Haltli B, Kerr RG, Ahmadi A. Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro-encapsulated marine bacteria. Biotechnol Bioeng 2020; 118:1166-1176. [PMID: 33241862 DOI: 10.1002/bit.27633] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/01/2020] [Accepted: 11/20/2020] [Indexed: 11/10/2022]
Abstract
Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high-throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single-cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or "Pod," that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.
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Affiliation(s)
- Tartela Alkayyali
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Emily Pope
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada
| | - Sydney K Wheatley
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
| | - Christopher Cartmell
- Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada
| | - Bradley Haltli
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Russell G Kerr
- Departments of Biomedical Sciences, University of Prince Edward Island, Prince Edward Island, Canada.,Departments of Chemistry, University of Prince Edward Island, Prince Edward Island, Canada.,Nautilus Biosciences Croda, Prince Edward Island, Canada
| | - Ali Ahmadi
- Faculty of Sustainable Design Engineering, University of Prince Edward Island, Prince Edward Island, Canada
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19
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Li SL, Wu HC, Hwang TL, Lin CH, Yang SS, Chang HS. Phytochemical Investigation and Anti-Inflammatory Activity of the Leaves of Machilus japonica var. kusanoi. Molecules 2020; 25:molecules25184149. [PMID: 32927887 PMCID: PMC7570621 DOI: 10.3390/molecules25184149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/02/2020] [Accepted: 09/05/2020] [Indexed: 12/05/2022] Open
Abstract
In a series of anti-inflammatory screenings of lauraceous plants, the methanolic extract of the leaves of Machilus japonica var. kusanoi (Hayata) J.C. Liao showed potent inhibition on both superoxide anion generation and elastase release in human neutrophils. Bioassay-guided fractionation of the leaves of M. japonica var. kusanoi led to the isolation of twenty compounds, including six new butanolides, machinolides A–F (1–6), and fourteen known compounds (7–20). Their structures were characterized by 1D and 2D NMR, UV, IR, CD, and MS data. The absolute configuration of the new compounds were unambiguously confirmed by single-crystal X-ray diffraction analyses (1, 2, and 3) and Mosher’s method (4, 5, and 6). In addition, lignans, (+)-eudesmin (11), (+)-methylpiperitol (12), (+)-pinoresinol (13), and (+)-galbelgin (16) exhibited inhibitory effects on N-formyl-methionyl-leucyl-phenylalanine/cytochalasin B (fMLP/CB)-induced superoxide anion generation in human neutrophils with IC50 values of 8.71 ± 0.74 μM, 2.23 ± 0.92 μM, 6.81 ± 1.07 μM, and 7.15 ± 2.26 μM, respectively. The results revealed the anti-inflammatory potentials of Formosan Machilus japonica var. kusanoi.
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Affiliation(s)
- Shiou-Ling Li
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (S.-L.L.); (S.-S.Y.)
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ho-Cheng Wu
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Research Center for Industry of Human Ecology, Research Center for Chinese Herbal Medicine, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chu-Hung Lin
- Botanical Drug Technology Division, Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 300, Taiwan;
| | - Shuen-Shin Yang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (S.-L.L.); (S.-S.Y.)
| | - Hsun-Shuo Chang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (S.-L.L.); (S.-S.Y.)
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-312-1101 (ext. 2664)
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20
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van Bergeijk DA, Terlouw BR, Medema MH, van Wezel GP. Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nat Rev Microbiol 2020; 18:546-558. [DOI: 10.1038/s41579-020-0379-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 01/09/2023]
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21
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Actinomycetes from the Red Sea Sponge Coscinoderma mathewsi: Isolation, Diversity, and Potential for Bioactive Compounds Discovery. Microorganisms 2020; 8:microorganisms8050783. [PMID: 32456212 PMCID: PMC7285244 DOI: 10.3390/microorganisms8050783] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
The diversity of actinomycetes associated with the marine sponge Coscinoderma mathewsi collected from Hurghada (Egypt) was studied. Twenty-three actinomycetes were separated and identified based on the 16S rDNA gene sequence analysis. Out of them, three isolates were classified as novel species of the genera Micromonospora, Nocardia, and Gordonia. Genome sequencing of actinomycete strains has revealed many silent biosynthetic gene clusters and has shown their exceptional capacity for the production of secondary metabolites, not observed under classical cultivation conditions. Therefore, the effect of mycolic-acid-containing bacteria or mycolic acid on the biosynthesis of cryptic natural products was investigated. Sponge-derived actinomycete Micromonospora sp. UA17 was co-cultured using liquid fermentation with two mycolic acid-containing actinomycetes (Gordonia sp. UA19 and Nocardia sp. UA 23), or supplemented with pure mycolic acid. LC-HRESIMS data were analyzed to compare natural production across all crude extracts. Micromonospora sp. UA17 was rich with isotetracenone, indolocarbazole, and anthracycline analogs. Some co-culture extracts showed metabolites such as a chlorocardicin, neocopiamycin A, and chicamycin B that were not found in the respective monocultures, suggesting a mycolic acid effect on the induction of cryptic natural product biosynthetic pathways. The antibacterial, antifungal, and antiparasitic activities for the different cultures extracts were also tested.
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22
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Bhattarai K, Bastola R, Baral B. Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance. ADVANCES IN GENETICS 2020; 105:229-292. [PMID: 32560788 DOI: 10.1016/bs.adgen.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.
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Affiliation(s)
- Keshab Bhattarai
- University of Tübingen, Tübingen, Germany; Center for Natural and Applied Sciences (CENAS), Kathmandu, Nepal
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal.
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23
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Abstract
Over a long period of time, humans have explored many natural resources looking for remedies of various ailments. Traditional medicines have played an intrinsic role in human life for thousands of years, with people depending on medicinal plants and their products as dietary supplements as well as using them therapeutically for treatment of chronic disorders, such as cancer, malaria, diabetes, arthritis, inflammation, and liver and cardiac disorders. However, plant resources are not sufficient for treatment of recently emerging diseases. In addition, the seasonal availability and other political factors put constrains on some rare plant species. The actual breakthrough in drug discovery came concurrently with the discovery of penicillin from Penicillium notatum in 1929. This discovery dramatically changed the research of natural products and positioned microbial natural products as one of the most important clues in drug discovery due to availability, variability, great biodiversity, unique structures, and the bioactivities produced. The number of commercially available therapeutically active compounds from microbial sources to date exceeds those discovered from other sources. In this review, we introduce a short history of microbial drug discovery as well as certain features and recent research approaches, specifying the microbial origin, their featured molecules, and the diversity of the producing species. Moreover, we discuss some bioactivities as well as new approaches and trends in research in this field.
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24
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Zhang C, Straight PD. Antibiotic discovery through microbial interactions. Curr Opin Microbiol 2019; 51:64-71. [DOI: 10.1016/j.mib.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/20/2019] [Indexed: 01/09/2023]
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25
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Jomori T, Hara Y, Sasaoka M, Harada K, Setiawan A, Hirata K, Kimishima A, Arai M. Mycobacterium smegmatis alters the production of secondary metabolites by marine-derived Aspergillus niger. J Nat Med 2019; 74:76-82. [PMID: 31321600 DOI: 10.1007/s11418-019-01345-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022]
Abstract
It is generally accepted that fungi have a number of dormant gene clusters for the synthesis of secondary metabolites, and the activation of these gene clusters can expand the diversity of secondary metabolites in culture. Recent studies have revealed that the mycolic acid-containing bacterium Tsukamurella pulmonis activates dormant gene clusters in the bacterial genus Streptomyces. However, it is not clear whether the mycolic acid-containing bacteria activate dormant gene clusters of fungi. We performed co-culture experiments using marine-derived Aspergillus niger with Mycobacterium smegmatis, a mycolic acid-containing bacteria. The co-cultivation resulted in the production of a pigment by A. niger and increased cytotoxic activity of the extract against human prostate cancer DU145 cells. An analysis of secondary metabolites in the extract of the co-culture broth revealed that the increase in cytotoxic activity was caused by the production of malformin C (1), and that TMC-256A1 (2), desmethylkotanin (3), and aurasperone C (4) were selectively produced under co-culture conditions. In addition, further study suggested that direct interaction between the two microorganisms was necessary for the production of the pigment and the cytotoxic compound malformin C (1) from A. niger. Given the biological activities of malformin C, including cytotoxic activity, our approach for increasing the production of bioactive secondary metabolites has important practical applications and may facilitate structural analyses of novel bioactive compounds.
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Affiliation(s)
- Takahiro Jomori
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - Yasumasa Hara
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - Miho Sasaoka
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - Kazuo Harada
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan.,Graduate School of Medicine, Osaka University, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Andi Setiawan
- Department of Chemistry, Faculty of Science, Lampung University, Jl. Prof. Dr. Sumantri Brodjonegoro No. 1, Bandar Lampung, 35145, Indonesia
| | - Kazumasa Hirata
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - Atsushi Kimishima
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka, 565-0871, Japan.
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26
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Yu M, Li Y, Banakar SP, Liu L, Shao C, Li Z, Wang C. New Metabolites From the Co-culture of Marine-Derived Actinomycete Streptomyces rochei MB037 and Fungus Rhinocladiella similis 35. Front Microbiol 2019; 10:915. [PMID: 31134000 PMCID: PMC6514141 DOI: 10.3389/fmicb.2019.00915] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/10/2019] [Indexed: 12/24/2022] Open
Abstract
Co-culture of different microbes simulating the natural state of microbial community may produce potentially new compounds because of nutrition or space competition. To mine its metabolic potential in depth, co-culture of Streptomyces rochei MB037 with a gorgonian-derived fungus Rhinocladiella similis 35 was carried out to stimulate the production of new metabolites in this study, using pure cultivation as control. Five metabolites were isolated successfully from co-culture broth, including two new fatty acids with rare nitrile group, borrelidins J and K (1 and 2), one chromone derivative as a new natural product, 7-methoxy-2,3-dimethylchromone-4-one (3), together with two known 18-membered macrolides, borrelidin (4) and borrelidin F (5). The structures of 1–3 were elucidated by using a combination of NMR and MS spectroscopy, ester hydrolysis, and optical rotation methods. Interestingly, 1 and 2 were obtained only in co-culture. Though 3 was gained from either co-culture or single culture, its production was increased significantly by co-culture. Compound 1 exhibited significant antibacterial activity against methicillin-resistant Staphylococcus aureus with a MIC value of 0.195 μg/mL.
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Affiliation(s)
- Meilin Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yingxin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shivakumar P Banakar
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Changlun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changyun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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27
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Mouncey NJ, Otani H, Udwary D, Yoshikuni Y. New voyages to explore the natural product galaxy. J Ind Microbiol Biotechnol 2019; 46:273-279. [PMID: 30610411 DOI: 10.1007/s10295-018-02122-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/19/2018] [Indexed: 12/01/2022]
Abstract
Natural products are a large family of diverse and complex chemical molecules that have roles in both primary and secondary metabolism, and over 210,000 natural products have been described. Secondary metabolite natural products are of high commercial and societal value with therapeutic uses as antibiotics, antifungals, antitumor and antiparasitic products and in agriculture as products for crop protection and animal health. There is a resurgence of activity in exploring natural products for a wide range of applications, due to not only increasing antibiotic resistance, but the advent of next-generation genome sequencing and new technologies to interrogate and investigate natural product biosynthesis. Genome mining has revealed a previously undiscovered richness of biosynthetic potential in novel biosynthetic gene clusters for natural products. Complementing these computational processes are new experimental platforms that are being developed and deployed to access new natural products.
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Affiliation(s)
- Nigel J Mouncey
- United States Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Hiroshi Otani
- United States Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Daniel Udwary
- United States Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Yasuo Yoshikuni
- United States Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
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Ozaki T, Sugiyama R, Shimomura M, Nishimura S, Asamizu S, Katsuyama Y, Kakeya H, Onaka H. Identification of the common biosynthetic gene cluster for both antimicrobial streptoaminals and antifungal 5-alkyl-1,2,3,4-tetrahydroquinolines. Org Biomol Chem 2019; 17:2370-2378. [DOI: 10.1039/c8ob02846j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The new subfamily of type II PKS gene cluster is responsible for biosynthesis of structurally distinct streptoaminals (STAMs) and 5-alkyl-1,2,3,4-tetrahydroquinolines (5aTHQs).
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Affiliation(s)
- Taro Ozaki
- Department of Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular Sciences
- Division of Bioinformatics and Chemical Genomics Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Morito Shimomura
- Department of Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences
- Division of Bioinformatics and Chemical Genomics Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Shumpei Asamizu
- Department of Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
- Collaborative Research Institute for Innovative Microbiology
| | - Yohei Katsuyama
- Department of Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
- Collaborative Research Institute for Innovative Microbiology
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences
- Division of Bioinformatics and Chemical Genomics Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroyasu Onaka
- Department of Biotechnology
- The University of Tokyo
- Bunkyo-ku
- Japan
- Collaborative Research Institute for Innovative Microbiology
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29
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Zhou Y, Li YH, Yu HB, Liu XY, Lu XL, Jiao BH. Furanone derivative and sesquiterpene from Antarctic marine-derived fungus Penicillium sp. S-1-18. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2018; 20:1108-1115. [PMID: 28990801 DOI: 10.1080/10286020.2017.1385604] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/24/2017] [Indexed: 06/07/2023]
Abstract
A new furanone derivative, butanolide A (1), and a new sesquiterpene, guignarderemophilane F (2), together with six known compounds, were isolated from the fungus Penicillium sp. S-1-18 derived from Antarctic marine. The new structures were determined by spectroscopic studies such as 1D- and 2D-NMR and MS analyses. The absolute configuration of 1 was determined by the modified Mosher's method, while the absolute configuration of 2 was determined by calculated ECD spectroscopy. The isolated secondary metabolites were evaluated for their protein tyrosine phosphatase 1B (PTP1B) inhibitory activity. Compound 1 showed moderate inhibitory activity against PTP1B with IC50 value of 27.4 μM.
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Affiliation(s)
- Yue Zhou
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
| | - Yun-Hai Li
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
| | - Hao-Bing Yu
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
| | - Xiao-Yu Liu
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
| | - Xiao-Ling Lu
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
| | - Bing-Hua Jiao
- a Marine Biopharmaceutical Institute , Second Military Medical University , Shanghai 200433 , China
- b Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences , Second Military Medical University , Shanghai 200433 , China
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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: 37] [Impact Index Per Article: 6.2] [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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Shin D, Byun WS, Moon K, Kwon Y, Bae M, Um S, Lee SK, Oh DC. Coculture of Marine Streptomyces sp. With Bacillus sp. Produces a New Piperazic Acid-Bearing Cyclic Peptide. Front Chem 2018; 6:498. [PMID: 30406080 PMCID: PMC6201156 DOI: 10.3389/fchem.2018.00498] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial culture conditions in the laboratory, which conventionally involve the cultivation of one strain in one culture vessel, are vastly different from natural microbial environments. Even though perfectly mimicking natural microbial interactions is virtually impossible, the cocultivation of multiple microbial strains is a reasonable strategy to induce the production of secondary metabolites, which enables the discovery of new bioactive natural products. Our coculture of marine Streptomyces and Bacillus strains isolated together from an intertidal mudflat led to discover a new metabolite, dentigerumycin E (1). Dentigerumycin E was determined to be a new cyclic hexapeptide incorporating three piperazic acids, N-OH-Thr, N-OH-Gly, β-OH-Leu, and a pyran-bearing polyketide acyl chain mainly by analysis of its NMR and MS spectroscopic data. The putative PKS-NRPS biosynthetic gene cluster for dentigerumycin E was found in the Streptomyces strain, providing clear evidence that this cyclic peptide is produced by the Streptomyces strain. The absolute configuration of dentigerumycin E was established based on the advanced Marfey's method, ROESY NMR correlations, and analysis of the amino acid sequence of the ketoreductase domain in the biosynthetic gene cluster. In biological evaluation of dentigerumycin E (1) and its chemical derivatives [2-N,16-N-deoxydenteigerumycin E (2) and dentigerumycin methyl ester (3)], only dentigerumycin E exhibited antiproliferative and antimetastatic activities against human cancer cells, indicating that N-OH and carboxylic acid functional groups are essential for the biological activity.
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Affiliation(s)
- Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Kyuho Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sang Kook Lee
- 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
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Wang W, Zeng F, Bie Q, Dai C, Chen C, Tong Q, Liu J, Wang J, Zhou Y, Zhu H, Zhang Y. Cytochathiazines A–C: Three Merocytochalasans with a 2H-1,4-Thiazine Functionality from Coculture of Chaetomium globosum and Aspergillus flavipes. Org Lett 2018; 20:6817-6821. [DOI: 10.1021/acs.orglett.8b02942] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wenjing Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Fanrong Zeng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Qiong Bie
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Chong Dai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Qingyi Tong
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Junjun Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Yuan Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People’s Republic of China
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Hagihara R, Katsuyama Y, Sugai Y, Onaka H, Ohnishi Y. Novel desferrioxamine derivatives synthesized using the secondary metabolism-specific nitrous acid biosynthetic pathway in Streptomyces davawensis. J Antibiot (Tokyo) 2018; 71:911-919. [PMID: 30120394 DOI: 10.1038/s41429-018-0088-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 01/02/2023]
Abstract
Recently, a novel nitrous acid biosynthetic pathway composed of two enzymes was discovered to be involved in the biosynthesis of cremeomycin for the formation of its diazo group. In this pathway, CreE oxidizes L-aspartic acid to nitrosuccinic acid and CreD liberates nitrous acid from nitrosuccinic acid. Bioinformatic analysis showed that various actinobacteria have putative secondary metabolite biosynthesis gene clusters containing creE and creD homologs, suggesting that this pathway is widely used for the biosynthesis of various natural products. Here, we focused on creE and creD homologs (BN159_4422 and BN159_4421) in Streptomyces davawensis. In vitro analysis of recombinant BN159_4422 and BN159_4421 proteins showed that these enzymes synthesized nitrous acid from L-aspartic acid. Secondary metabolites produced by this gene cluster were investigated by comparing the metabolic profiles of the wild-type and ΔBN159_4422 strains. When these strains were co-cultured with Tsukamurella pulmonis TP-B0596, three compounds were specifically produced by the wild-type strain. These compounds were identified as novel desferrioxamine derivatives containing either of two unique five-membered heterocyclic ring structures and shown to have iron-binding properties. A putative desferrioxamine biosynthetic gene cluster was found in the S. davawensis genome, and inactivation of a desD homolog (BN159_5485) also abolished the production of these compounds. We propose that these compounds should be synthesized by the modification of desferrioxamine B and a shorter chain analog using nitrous acid produced by the CreE and CreD homologs. This study provides an important insight into the diverse usage of the secondary metabolism-specific nitrous acid biosynthetic pathway in actinomycetes.
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Affiliation(s)
- Ryota Hagihara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Yoshinori Sugai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Wang W, Gong J, Liu X, Dai C, Wang Y, Li XN, Wang J, Luo Z, Zhou Y, Xue Y, Zhu H, Chen C, Zhang Y. Cytochalasans Produced by the Coculture of Aspergillus flavipes and Chaetomium globosum. JOURNAL OF NATURAL PRODUCTS 2018; 81:1578-1587. [PMID: 29969028 DOI: 10.1021/acs.jnatprod.8b00110] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The cocultivation of Aspergillus flavipes and Chaetomium globosum, rich sources of cytochalasans, on solid rice medium, resulted in the production of 13 new, highly oxygenated cytochalasans, aspochalasinols A-D (1-4) and oxichaetoglobosins A-I (5-13), as well as seven known compounds (14-20). Of these compounds, 13 is a novel cytochalasan with an unexpected 2-norindole group. The isolated compounds were characterized by NMR spectroscopy, single-crystal X-ray crystallography, and ECD experiments. Compounds 1-4 represent the first examples of Asp-type cytochalasans with C-12 hydroxy groups, which may be a result of the coculture, as hydroxylated Me-12 groups are frequently found in Chae-type cytochalasans from C. globosum. In addition, 5-10 are unusual cytochalasans with an oxygenated C-10. Interestingly, 13 is the first example of a naturally occurring cytochalasan possessing a uniquely degraded indole ring that is derived from chaetoglobosin W, with 11 and 12 both serving as its biosynthetic intermediates. In the coculture of A. flavipes and C. globosum, most of these cytochalasans are more functionalized than normal cytochalasans, and the underlying causes may attract substantial attention from synthetic biologists. The cytotoxicities against five human cancer cell lines (SW480, HL-60, A549, MCF-7, and SMMC-7721) and the immunomodulatory activities of these new compounds were evaluated in vitro.
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Affiliation(s)
- Wenjing Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Jiaojiao Gong
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Xiaorui Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Chong Dai
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Yanyan Wang
- First College of Clinical Medical Science , China Three Gorges University & Yichang Central People's Hospital , Yichang 443003 , People's Republic of China
| | - Xiao-Nian Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany , Chinese Academy of Sciences , Kunming 650204 , People's Republic of China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Zengwei Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Yuan Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Yongbo Xue
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy , Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
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Antibiotic discovery: combining isolation chip (iChip) technology and co-culture technique. Appl Microbiol Biotechnol 2018; 102:7333-7341. [DOI: 10.1007/s00253-018-9193-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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Hoshino S, Okada M, Awakawa T, Asamizu S, Onaka H, Abe I. Mycolic Acid Containing Bacterium Stimulates Tandem Cyclization of Polyene Macrolactam in a Lake Sediment Derived Rare Actinomycete. Org Lett 2017; 19:4992-4995. [DOI: 10.1021/acs.orglett.7b02508] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shotaro Hoshino
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Okada
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shumpei Asamizu
- Graduate
School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyasu Onaka
- Graduate
School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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37
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Upregulation and Identification of Antibiotic Activity of a Marine-Derived Streptomyces sp. via Co-Cultures with Human Pathogens. Mar Drugs 2017; 15:md15080250. [PMID: 28800088 PMCID: PMC5577605 DOI: 10.3390/md15080250] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/04/2023] Open
Abstract
Marine natural product drug discovery has begun to play an important role in the treatment of disease, with several recently approved drugs. In addition, numerous microbial natural products have been discovered from members of the order Actinomycetales, particularly in the genus Streptomyces, due to their metabolic diversity for production of biologically active secondary metabolites. However, many secondary metabolites cannot be produced under laboratory conditions because growth conditions in flask culture differ from conditions in the natural environment. Various experimental conditions (e.g., mixed fermentation) have been attempted to increase yields of previously described metabolites, cause production of previously undetected metabolites, and increase antibiotic activity. Adult ascidians-also known as tunicates-are sessile marine invertebrates, making them vulnerable to predation and therefore are hypothesized to use host-associated bacteria that produce biologically active secondary metabolites for chemical defense. A marine-derived Streptomyces sp. strain PTY087I2 was isolated from a Panamanian tunicate and subsequently co-cultured with human pathogens including Bacillus subtilis, methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA), and Pseudomonas aeruginosa, followed by extraction. Co-culture of Streptomyces sp. PTY087I2 with each of these human pathogens resulted in increased production of three antibiotics: granaticin, granatomycin D, and dihydrogranaticin B, as well as several analogues seen via molecular networking. In addition, co-cultures resulted in strongly enhanced biological activity against the Gram positive human pathogens used in these experiments. Expanded utilization of co-culture experiments to allow for competitive interactions may enhance metabolite production and further our understanding of these microbial interactions.
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Abstract
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.
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Affiliation(s)
- Navid Adnani
- University of Wisconsin Madison, School of Pharmacy, Div. of Pharmaceutical Sciences, 777 Highland Ave., Madison, WI 53705-2222, USA.
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Novel antibiotic screening methods to awaken silent or cryptic secondary metabolic pathways in actinomycetes. J Antibiot (Tokyo) 2017; 70:865-870. [DOI: 10.1038/ja.2017.51] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022]
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40
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Antibiotics in microbial coculture. J Antibiot (Tokyo) 2016; 70:361-365. [DOI: 10.1038/ja.2016.127] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 12/28/2022]
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41
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Sugiyama R, Nishimura S, Ozaki T, Asamizu S, Onaka H, Kakeya H. Discovery and Total Synthesis of Streptoaminals: Antimicrobial [5,5]-Spirohemiaminals from the Combined-Culture of Streptomyces nigrescens
and Tsukamurella pulmonis. Angew Chem Int Ed Engl 2016; 55:10278-82. [DOI: 10.1002/anie.201604126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
- Present address; RIKEN Center for Sustainable Resource Science; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
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42
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Sugiyama R, Nishimura S, Ozaki T, Asamizu S, Onaka H, Kakeya H. Discovery and Total Synthesis of Streptoaminals: Antimicrobial [5,5]-Spirohemiaminals from the Combined-Culture of Streptomyces nigrescens
and Tsukamurella pulmonis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryosuke Sugiyama
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
- Present address; RIKEN Center for Sustainable Resource Science; 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama Kanagawa 230-0045 Japan
| | - Shinichi Nishimura
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo 113-8657 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
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43
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Hoshino S, Okada M, Onaka H, Abe I. Effective Production of Aromatic Polyketides in Streptomyces using a Combined-Culture Method. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Combined-culture is a fermentation method which efficiently induces secondary metabolite production in Streptomyces by co-culturing them with mycolic acid-containing bacteria. As a result of combined-culture screening of our terrestrial Streptomyces collection using UV-HPLC, one of the tested strains, Streptomyces sp. TAKO-2, produced two known aromatic polyketides, julichrome Q6 (1) and julichrome Q8·8 (2), when co-cultured with the mycolic acid-containing bacterium Tsukamurella pulmonis TP-B0596. The structures of 1 and 2 were confirmed by spectroscopic analysis and literature data.
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Affiliation(s)
- Shotaro Hoshino
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Okada
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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44
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Du D, Katsuyama Y, Onaka H, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Production of a Novel Amide-Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster inStreptomycessp. MSC090213JE08. Chembiochem 2016; 17:1464-71. [DOI: 10.1002/cbic.201600167] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Danyao Du
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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45
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Zhang XM, Zhang DF, Li WJ, Lu CH. Pseudonocardides A - G, Newγ-Butyrolactones from Marine-derivedPseudonocardiasp. YIM M13669. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xiao-Mei Zhang
- Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
- Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; No. 44 West Wenhua Road Jinan 250012 P. R. China
| | - Dao-Feng Zhang
- Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
| | - Wen-Jun Li
- Yunnan Institute of Microbiology; Yunnan University; Kunming 650091 P. R. China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-Sen University; Guangzhou 510275 P. R. China
| | - Chun-Hua Lu
- Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; No. 44 West Wenhua Road Jinan 250012 P. R. China
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46
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Hoshino S, Okada M, Wakimoto T, Zhang H, Hayashi F, Onaka H, Abe I. Niizalactams A-C, Multicyclic Macrolactams Isolated from Combined Culture of Streptomyces with Mycolic Acid-Containing Bacterium. JOURNAL OF NATURAL PRODUCTS 2015; 78:3011-3017. [PMID: 26624939 DOI: 10.1021/acs.jnatprod.5b00804] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A terrestrial bacterium, Streptomyces sp. NZ-6, produced niizalactams A-C (1-3), unprecedented di- and tricyclic macrolactams, by coculturing with the mycolic acid-containing bacterium Tsukamurella pulmonis TP-B0596. Their complete structures, including absolute configurations, were elucidated on the basis of spectroscopic data and chemical derivatization. Their unique skeletons are proposed to be biosynthesized from a common 26-membered macrolactam intermediate by SN2 cyclization or an intramolecular Diels-Alder reaction.
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Affiliation(s)
- Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Okada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
| | - Huiping Zhang
- RIKEN Center for Life Science Technologies , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Fumiaki Hayashi
- RIKEN Center for Life Science Technologies , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-0033, Japan
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47
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Asamizu S, Ozaki T, Teramoto K, Satoh K, Onaka H. Killing of Mycolic Acid-Containing Bacteria Aborted Induction of Antibiotic Production by Streptomyces in Combined-Culture. PLoS One 2015; 10:e0142372. [PMID: 26544713 PMCID: PMC4636228 DOI: 10.1371/journal.pone.0142372] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/21/2015] [Indexed: 02/02/2023] Open
Abstract
Co-culture of Streptomyces with mycolic acid-containing bacteria (MACB), which we termed “combined-culture,” alters the secondary metabolism pattern in Streptomyces and has been a useful method for the discovery of bioactive natural products. In the course of our investigation to identify the inducing factor(s) of MACB, we previously observed that production of pigments in Streptomyces lividans was not induced by factors such as culture extracts or mycolic acids. Although dynamic changes occurred in culture conditions because of MACB, the activation of pigment production by S. lividans was observed in a limited area where both colonies were in direct contact. This suggested that direct attachment of cells is a requirement and that components on the MACB cell membrane may play an important role in the response by S. lividans. Here we examined whether this response was influenced by dead MACB that possess intact mycolic acids assembled on the outer cell membrane. Formaldehyde fixation and γ-irradiation were used to prepare dead cells that retain their shape and mycolic acids of three MACB species: Tsukamurella pulmonis, Rhodococcus erythropolis, and Rhodococcus opacus. Culturing tests verified that S. lividans does not respond to the intact dead cells of three MACB. Observation of combined-culture by scanning electron microscopy (SEM) indicated that adhesion of live MACB to S. lividans mycelia were a significant interaction that resulted in formation of co-aggregation. In contrast, in the SEM analysis, dead cells were not observed to adhere. Therefore, direct attachment by live MACB cells is proposed as one of the possible factors that causes Streptomyces to alter its specialized metabolism in combined-culture.
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Affiliation(s)
- Shumpei Asamizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
| | - Taro Ozaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kanae Teramoto
- Advanced Technology Department, JEOL Ltd., Akishima, Tokyo, Japan
| | - Katsuya Satoh
- Ion Beam Mutagenesis Research Group, Biotechnology and Medical Application Division, Quantum Beam Science Center, Japan Atomic Energy Agency, Takasaki, Gunma, Japan
| | - Hiroyasu Onaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail: (SA); (HO)
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Investigation of Interspecies Interactions within Marine Micromonosporaceae Using an Improved Co-Culture Approach. Mar Drugs 2015; 13:6082-98. [PMID: 26404321 PMCID: PMC4626680 DOI: 10.3390/md13106082] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/16/2022] Open
Abstract
With respect to bacterial natural products, a significant outcome of the genomic era was that the biosynthetic potential in many microorganisms surpassed the number of compounds isolated under standard laboratory growth conditions, particularly among certain members in the phylum Actinobacteria. Our group, as well as others, investigated interspecies interactions, via co-culture, as a technique to coax bacteria to produce novel natural products. While co-culture provides new opportunities, challenges exist and questions surrounding these methods remain unanswered. In marine bacteria, for example, how prevalent are interspecies interactions and how commonly do interactions result in novel natural products? In an attempt to begin to answer basic questions surrounding co-culture of marine microorganisms, we have tested both antibiotic activity-based and LC/MS-based methods to evaluate Micromonosporaceae secondary metabolite production in co-culture. Overall, our investigation of 65 Micromonosporaceae led to the identification of 12 Micromonosporaceae across three genera that produced unique metabolites in co-culture. Our results suggest that interspecies interactions were prevalent between marine Micromonosporaceae and marine mycolic acid-containing bacteria. Furthermore, our approach highlights a sensitive and rapid method for investigating interspecies interactions in search of novel antibiotics, secondary metabolites, and genes.
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Metabolic profiling as a tool for prioritizing antimicrobial compounds. J Ind Microbiol Biotechnol 2015; 43:299-312. [PMID: 26335567 PMCID: PMC4752588 DOI: 10.1007/s10295-015-1666-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/25/2015] [Indexed: 11/29/2022]
Abstract
Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.
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