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Boruta T, Englart G, Foryś M, Pawlikowska W. The repertoire and levels of secondary metabolites in microbial cocultures depend on the inoculation ratio: a case study involving Aspergillus terreus and Streptomyces rimosus. Biotechnol Lett 2024; 46:601-614. [PMID: 38844646 PMCID: PMC11217084 DOI: 10.1007/s10529-024-03500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/10/2024] [Accepted: 05/18/2024] [Indexed: 07/03/2024]
Abstract
OBJECTIVE The aim of this study was to determine the influence of the inoculation volume ratio on the production of secondary metabolites in submerged cocultures of Aspergillus terreus and Streptomyces rimosus. RESULTS The shake flask cocultures were initiated by using 23 inoculum variants that included different volumes of A. terreus and S. rimosus precultures. In addition, the axenic controls were propagated in parallel with the cocultures. UPLC‒MS analysis revealed the presence of 15 secondary metabolites, 12 of which were found both in the "A. terreus vs. S. rimosus" cocultures and axenic cultures of either A. terreus or S. rimosus. The production of the remaining 3 molecules was recorded solely in the cocultures. The repertoire and quantity of secondary metabolites were evidently dependent on the inoculation ratio. It was also noted that detecting filamentous structures resembling typical morphological forms of a given species was insufficient to predict the presence of a given metabolite. CONCLUSIONS The modification of the inoculation ratio is an effective strategy for awakening and enhancing the production of secondary metabolites that are not biosynthesized under axenic conditions.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland.
| | - Grzegorz Englart
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
| | - Martyna Foryś
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
| | - Weronika Pawlikowska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wólczańska 213, 93-005, Lodz, Poland
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2
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Díaz-Cruz GA, Bignell DRD. Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2. Sci Rep 2024; 14:10414. [PMID: 38710735 DOI: 10.1038/s41598-024-60630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
- Phytopathology Department, Plant Protection Research Center (CIPROC), Agronomy School, Universidad de Costa Rica, San Jose, Costa Rica
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
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3
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Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun 2023; 14:3390. [PMID: 37296102 PMCID: PMC10256842 DOI: 10.1038/s41467-023-38859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchic workflow to focus on specific targets based on analysis of metabolomics data and growth rescue experiments. We deploy this framework to understand the intracellular molecular interactions of the multi-valent dihydrofolate reductase-targeting antibiotic compound CD15-3. We analyse global metabolomics data utilizing machine learning, metabolic modelling, and protein structural similarity to prioritize candidate drug targets. Overexpression and in vitro activity assays confirm one of the predicted candidates, HPPK (folK), as a CD15-3 off-target. This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.
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Affiliation(s)
- Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joao V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens Lyngby, Denmark
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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Wang DG, Wang CY, Hu JQ, Wang JJ, Liu WC, Zhang WJ, Du XR, Wang H, Zhu LL, Sui HY, Li YZ, Wu C. Constructing a Myxobacterial Natural Product Database to Facilitate NMR-Based Metabolomics Bioprospecting of Myxobacteria. Anal Chem 2023; 95:5256-5266. [PMID: 36917632 DOI: 10.1021/acs.analchem.2c05145] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Myxobacteria are fascinating prokaryotes featuring a potent capacity for producing a wealth of bioactive molecules with intricate chemical topology as well as intriguing enzymology, and thus it is critical to developing an efficient pipeline for bioprospecting. Herein, we construct the database MyxoDB, the first public compendium solely dedicated to myxobacteria, which enabled us to provide an overview of the structural diversity and taxonomic distribution of known myxobacterial natural products. Moreover, we demonstrated that the cutting-edge NMR-based metabolomics was effective to differentiate the biosynthetic priority of myxobacteria, whereby MyxoDB could greatly streamline the dereplication of multifarious known compounds and accordingly speed up the discovery of new compounds. This led to the rapid identification of a class of linear di-lipopeptides (archangimins) and a rare rearranged sterol (corasterol) that were endowed with unique chemical architectures and/or biosynthetic enzymology. We also showcased that NMR-based metabolomics, MyxoDB, and genomics can also work concertedly to accelerate the targeted discovery of a polyketidic compound pyxipyrrolone C. All in all, this study sets the stage for the discovery of many more novel natural products from underexplored myxobacterial resources.
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Affiliation(s)
- De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Chao Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Wen-Juan Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xin-Ran Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Han Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hai-Yan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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Chi Y, Sun W, Zhou L, Pei S, Zeng H, Cheng Y, Chai S. The preparation of hybrid silicon quantum dots by one-step synthesis for tetracycline detection and antibacterial applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1145-1156. [PMID: 36787098 DOI: 10.1039/d2ay02102a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In this study, we prepared three different silicon quantum dots (SiQDs-1, SiQDs-2 and SiQDs-3) by hydrothermal synthesis with rose Bengal as the reducing agent and triacetoxy(methyl)silane and allyloxytrimethylsilane as silicon sources. The as-prepared SiQDs not only exhibited potent antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) but also showed specific responses to tetracycline (TC). The minimum inhibitory concentrations (MICs) of SiQDs-1, SiQDs-2 and SiQDs-3 were 0.55 mg mL-1, 0.47 mg mL-1 and 0.39 mg mL-1 against E. coli, respectively, and 0.45 mg mL-1, 0.34 mg mL-1 and 0.34 mg mL-1 against S. aureus, respectively. By examining the morphologies of bacteria and generation of reactive oxygen species (ROS), we speculated that these SiQDs shrink the bacteria and even directly destroy the bacterial structural integrity through the production of singlet oxygen. In addition, the fluorescence quenching effectiveness of SiQDs-3 also showed a strong linear relationship with TC concentration in the range of 0-1.2 μM with a detection limit of 0.318 μM, as a result of the internal filtering effect. Together, SiQDs not only can be a candidate to treat resistant bacterial infections, but also may be applied in practical detection of TC.
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Affiliation(s)
- Yuting Chi
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
| | - Wanlin Sun
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
| | - Lijia Zhou
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
| | - Shuchen Pei
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
| | - Haichun Zeng
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
| | - Yunying Cheng
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, P. R. China.
| | - Shuiqin Chai
- Chongqing Key Laboratory of Industrial Fermentation Microorganism, Chongqing University of Science and Technology, Chongqing 401331, P. R. China.
- College of Chemistry and Chemical Engineering, Chongqing University of Science and Technology, Chongqing 401331, P. R. China
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Hussein HA, Kassim MNI, Maulidiani M, Abas F, Abdullah MA. Cytotoxicity and 1H NMR metabolomics analyses of microalgal extracts for synergistic application with Tamoxifen on breast cancer cells with reduced toxicity against Vero cells. Heliyon 2022; 8:e09192. [PMID: 35846482 PMCID: PMC9280575 DOI: 10.1016/j.heliyon.2022.e09192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/22/2022] [Accepted: 03/22/2022] [Indexed: 11/20/2022] Open
Abstract
This study evaluated the cytotoxic activity of Tamoxifen (TMX), an anti-estrogen drug, with microalgal crude extracts (MCEs) in single and synergistic application (TMX-MCEs) on MCF-7 and 4T1 breast cancer cells, and non-cancerous Vero cells. The MCEs of Nannochloropsis oculata, Tetraselmis suecica and Chlorella sp. from five different solvents (methanol, MET; ethanol, ETH; water, W; chloroform, CHL; and hexane, HEX) were developed. The TMX-MCEs-ETH and W at the 1:2 and 1:3 ratios, attained IC50 of 15.84-29.51 μg/mL against MCF-7; 13.8-31.62 μg/mL against 4T1; and 24.54-85.11 μg/mL against Vero cells. Higher late apoptosis was exhibited against MCF-7 by the TMX-N. oculata-ETH (41.15 %); and by the TMX-T. suecica-ETH (65.69 %) against 4T1 cells. The TMX-T. suecica-ETH also showed higher ADP/ATP ratios, but comparable Caspase activities to control. For Vero cells, overall apoptotic effects were lowered with synergistic application, and only early apoptosis was higher with TMX-T. suecica-ETH but at lower levels (29.84 %). The MCEs-W showed the presence of alanine, oleic acid, linoleic acid, lactic acid, and fumaric acid. Based on Principal Component Analysis (PCA), the spectral signals for polar solvents such as MET and ETH, were found in the same cluster, while the non-polar solvent CHL was with HEX, suggesting similar chemical profiles clustered for the same polarity. The CHL and HEX were more effective with N. oculata and T. suecica which were of the marine origin, while the ETH and MET were more effective with Chlorella sp., which was of the freshwater origin. The synergistic application of microalgal bioactive compounds with TMX can maintain the cytotoxicity against breast cancer cells whilst reducing the toxicity against non-cancerous Vero cells. These findings will benefit the biopharmaceutical, and functional and healthy food industries.
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Affiliation(s)
- Hanaa Ali Hussein
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- College of Dentistry, University of Basrah, Basrah, Iraq
| | - Murni Nur Islamiah Kassim
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - M. Maulidiani
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Faridah Abas
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohd Azmuddin Abdullah
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- SIBCo Medical and Pharmaceuticals Sdn. Bhd., No. 2, Level 5, Jalan Tengku Ampuan Zabedah, D9/D, Seksyen 9, 40000 Shah Alam, Selangor, Malaysia
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7
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Hu WF, Niu L, Yue XJ, Zhu LL, Hu W, Li YZ, Wu C. Characterization of Constitutive Promoters for the Elicitation of Secondary Metabolites in Myxobacteria. ACS Synth Biol 2021; 10:2904-2909. [PMID: 34757714 DOI: 10.1021/acssynbio.1c00444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genome mining has revealed that myxobacteria contain a myriad of cryptic biosynthetic gene clusters (BGCs). Here, we report the characterization of a panel of myxobacterial promoters with variable strength that are applicable in the engineering of BGCs in myxobacteria. The screened strongest constitutive promoter was used to efficiently enhance the expression of two complex BGCs governing the biosynthesis of myxochromide and DKxanthene in the model myxobacterium Myxococcus xanthus DK1622. We also showcased the combination of promoter engineering and MS2-based spectral networking as an effective strategy to shed light on the previously overlooked chemistry in the family of myxochromide-type lipopeptides. The enriched promoter library substantially expanded the synthetic biology toolkit available for myxobacteria.
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Affiliation(s)
- Wei-Feng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Luo Niu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
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8
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Comparative Metabolomics Reveals Fungal Conversion of Co-Existing Bacterial Metabolites within a Synthetic Aspergillus- Streptomyces Community. Mar Drugs 2021; 19:md19090526. [PMID: 34564188 PMCID: PMC8472691 DOI: 10.3390/md19090526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022] Open
Abstract
In nature, secondary metabolites have been proven to be the essential communication media between co-occurring microorganisms and to influence their relationship with each other. In this study, we conducted a metabolomics survey of the secondary metabolites of an artificial co-culture related to a hydrothermal vent fungal–bacterial community comprising Aspergillus sclerotiorum and Streptomyces and their reciprocal relationship. The fungal strain was found to increase the secretion of notoamides and the compound cyclo(Pro-Trp) produced by the actinomycetes strain was discovered to be the responsible molecule. This led to the hypothesis that the fungi transformed cyclo(Pro-Trp) synthesized by the actinomycetes as the biosynthetic precursors of notoamides in the chemical communication. Further analysis showed Streptomyces sp. WU20 was efficient in transforming amino acids into cyclo(Pro-Trp) and adding tryptophan as well as proline into the chemical communication enhanced the induction of the notoamide accumulation. Thus, we propose that the microbial transformation during the synthetic metabolically-mediated chemical communication might be a promising means of speeding up the discovery of novel bioactive molecules. The objective of this research was to clarify the mechanism of microbial transformation for the chemical communication. Besides, this research also highlights the utility of mass spectrometry-based metabolomics as an effective tool in the direct biochemical analysis of community metabolites.
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9
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Peng XY, Wu JT, Shao CL, Li ZY, Chen M, Wang CY. Co-culture: stimulate the metabolic potential and explore the molecular diversity of natural products from microorganisms. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:363-374. [PMID: 37073292 PMCID: PMC10077301 DOI: 10.1007/s42995-020-00077-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/11/2020] [Indexed: 05/03/2023]
Abstract
Microbial secondary metabolites have long been considered as potential sources of lead compounds for medicinal use due to their rich chemical diversity and extensive biological activities. However, many biosynthetic gene clusters remain silent under traditional laboratory culture conditions, resulting in repeated isolation of a large number of known compounds. The co-culture strategy simulates the complex ecological environment of microbial life by using an ecology-driven method to activate silent gene clusters of microorganisms and tap their metabolic potential to obtain novel bioactive secondary metabolites. In this review, representative studies from 2017 to 2020 on the discovery of novel bioactive natural products from co-cultured microorganisms are summarized. A series of natural products with diverse and novel structures have been discovered successfully by co-culture strategies, including fungus-fungus, fungus-bacterium, and bacterium-bacterium co-culture approaches. These novel compounds exhibited various bioactivities including extensive antimicrobial activities and potential cytotoxic activities, especially when it came to disparate marine-derived species and cross-species of marine strains and terrestrial strains. It could be concluded that co-culture can be an effective strategy to tap the metabolic potential of microorganisms, particularly for marine-derived species, thus providing diverse molecules for the discovery of lead compounds and drug candidates.
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Affiliation(s)
- Xiao-Yue Peng
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Marine Science and Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jin-Tao Wu
- Marine Science and Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127 China
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Zhi-Yong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 201100 China
| | - Min Chen
- Marine Science and Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127 China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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10
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Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani. Microbiol Res 2021; 251:126836. [PMID: 34371303 DOI: 10.1016/j.micres.2021.126836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/20/2022]
Abstract
The concern regarding the emergence of phytopathogens strains which are resistant to conventional agrochemicals has given support to the search for alternatives on the use of chemical pesticides in agriculture. In this context, microorganisms are considered as promising sources of useful natural compounds and actinobacteria are particularly relevant since they are known to produce several bioactive metabolites. The objective of this work was to investigate the production of secondary metabolites with antifungal activity by a strain of the actinobacteria Streptomyces lunalinharesii (A54A) under axenic conditions and in co-cultivation with the phytopathogen Rhizoctonia solani. Tests to evaluate antifungal activity of the extracts indicated the presence of diffusable molecules capable of inhibiting the growth of R. solani produced by S. lunalinharesii, especially when in the presence of the fungus during fermentation. Metabolomic analyzes allowed the putative annotation of the bioactive compounds desferrioxamine E and anisomycin, in addition to the evaluation of the metabolic profile of the isolate when grown in axenic mode and in co-cultivation, while statistical analyzes enabled the comparison of such profiles and the identification of metabolites produced in greater relative quantities in the elicitation condition. Such methodologies provided the selection of unknown features with high bioactive potential for dereplication, and several metabolites of S. lunalinharesii possibly represent novel compounds.
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Hu JQ, Wang JJ, Li YL, Zhuo L, Zhang A, Sui HY, Li XJ, Shen T, Yin Y, Wu ZH, Hu W, Li YZ, Wu C. Combining NMR-Based Metabolic Profiling and Genome Mining for the Accelerated Discovery of Archangiumide, an Allenic Macrolide from the Myxobacterium Archangium violaceum SDU8. Org Lett 2021; 23:2114-2119. [PMID: 33689374 DOI: 10.1021/acs.orglett.1c00265] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An unprecedented 19-membered allenic macrolide archangiumide (1) was discovered from the myxobacterium Archangium violaceum SDU8 by integrating NMR-based metabolic profiling and genome mining. Its biosynthesis pathway was proposed based on the architectural analysis of the encoding trans-AT PKS genes and validated by isotope labeling. The methodology of combing 2D NMR-based metabolic profiling and bioinformatics-aided structure prediction, as exemplified by this study, is anticipated to improve discovery efficiency of a broader range of microbial "dark matter".
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Affiliation(s)
- Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Jing-Jing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Yue-Lan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Ai Zhang
- Fetal Medicine Center, Qingdao Women and Children's Hospital, Qingdao University, 266071 Qingdao, P.R. China
| | - Hai-Yan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Xiao-Ju Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Tao Shen
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Shandong University, 250100 Jinan, PR China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Zhi-Hong Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China
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12
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Sebak M, Saafan AE, Abdelghani S, Bakeer W, Moawad AS, El-Gendy AO. Isolation and optimized production of putative antimicrobial compounds from Egyptian soil isolate Streptomyces sp. MS. 10. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-021-00099-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Abstract
Background
The rapid spread of antibiotic resistance has increased research interest in the discovery of natural products, mainly from actinomycetes, which have been the primary source of antimicrobial compounds. This study aimed to isolate, characterize, and optimize the production of some of the bioactive compounds from bioactive soil actinomycetes.
Results
One promising soil actinomycete, which was molecularly identified as Streptomyces sp. and designated as Streptomyces sp. MS. 10, showed broad-spectrum antimicrobial activity, including activity against methicillin-resistant Staphylococcus aureus. Thus, it was selected for isolation of its major bioactive compounds. Polymerase chain reaction amplification of the genes responsible for antibiotic biosynthesis showed the presence of genes encoding type I and type II polyketide synthase. Liquid chromatography-mass spectrometry analysis found that the major antimicrobial compounds produced by Streptomyces sp. MS. 10 were weakly ionized bioactive secondary metabolites. A large-scale fermentation experiment of Streptomyces sp. MS. 10 using pre-optimized culture conditions followed by bioassay-guided chromatographic separation of its secondary metabolites resulted in the isolation of putative bioactive compounds that were identified as fatty acids using proton nuclear magnetic resonance spectroscopy.
Conclusions
Egyptian soil is still a good source for exploring bioactive actinomycetes. Additionally, this study highlighted the importance of combining both physicochemical and genotypic characterization with spectroscopic analysis of the major natural products when isolating bioactive metabolites.
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13
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Lee N, Hwang S, Kim W, Lee Y, Kim JH, Cho S, Kim HU, Yoon YJ, Oh MK, Palsson BO, Cho BK. Systems and synthetic biology to elucidate secondary metabolite biosynthetic gene clusters encoded in Streptomyces genomes. Nat Prod Rep 2021; 38:1330-1361. [PMID: 33393961 DOI: 10.1039/d0np00071j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2010 to 2020 Over the last few decades, Streptomyces have been extensively investigated for their ability to produce diverse bioactive secondary metabolites. Recent advances in Streptomyces research have been largely supported by improvements in high-throughput technology 'omics'. From genomics, numerous secondary metabolite biosynthetic gene clusters were predicted, increasing their genomic potential for novel bioactive compound discovery. Additional omics, including transcriptomics, translatomics, interactomics, proteomics and metabolomics, have been applied to obtain a system-level understanding spanning entire bioprocesses of Streptomyces, revealing highly interconnected and multi-layered regulatory networks for secondary metabolism. The comprehensive understanding derived from this systematic information accelerates the rational engineering of Streptomyces to enhance secondary metabolite production, integrated with the exploitation of the highly efficient 'Design-Build-Test-Learn' cycle in synthetic biology. In this review, we describe the current status of omics applications in Streptomyces research to better understand the organism and exploit its genetic potential for higher production of valuable secondary metabolites and novel secondary metabolite discovery.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yeo Joon Yoon
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA. and Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea. and Innovative Biomaterials Centre, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea and Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Lyngby, 2800, Denmark
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14
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Schäfer AB, Wenzel M. A How-To Guide for Mode of Action Analysis of Antimicrobial Peptides. Front Cell Infect Microbiol 2020; 10:540898. [PMID: 33194788 PMCID: PMC7604286 DOI: 10.3389/fcimb.2020.540898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to classical antibiotics in the fight against multi-resistant bacteria. They are produced by organisms from all domains of life and constitute a nearly universal defense mechanism against infectious agents. No drug can be approved without information about its mechanism of action. In order to use them in a clinical setting, it is pivotal to understand how AMPs work. While many pore-forming AMPs are well-characterized in model membrane systems, non-pore-forming peptides are often poorly understood. Moreover, there is evidence that pore formation may not happen or not play a role in vivo. It is therefore imperative to study how AMPs interact with their targets in vivo and consequently kill microorganisms. This has been difficult in the past, since established methods did not provide much mechanistic detail. Especially, methods to study membrane-active compounds have been scarce. Recent advances, in particular in microscopy technology and cell biological labeling techniques, now allow studying mechanisms of AMPs in unprecedented detail. This review gives an overview of available in vivo methods to investigate the antibacterial mechanisms of AMPs. In addition to classical mode of action classification assays, we discuss global profiling techniques, such as genomic and proteomic approaches, as well as bacterial cytological profiling and other cell biological assays. We cover approaches to determine the effects of AMPs on cell morphology, outer membrane, cell wall, and inner membrane properties, cellular macromolecules, and protein targets. We particularly expand on methods to examine cytoplasmic membrane parameters, such as composition, thickness, organization, fluidity, potential, and the functionality of membrane-associated processes. This review aims to provide a guide for researchers, who seek a broad overview of the available methodology to study the mechanisms of AMPs in living bacteria.
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Affiliation(s)
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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Matroodi S, Siitonen V, Baral B, Yamada K, Akhgari A, Metsä-Ketelä M. Genotyping-Guided Discovery of Persiamycin A From Sponge-Associated Halophilic Streptomonospora sp. PA3. Front Microbiol 2020; 11:1237. [PMID: 32582127 PMCID: PMC7296137 DOI: 10.3389/fmicb.2020.01237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial natural products have been a cornerstone of the pharmaceutical industry, but the supply of novel bioactive secondary metabolites has diminished due to extensive exploration of the most easily accessible sources, namely terrestrial Streptomyces species. The Persian Gulf is a unique habitat for marine sponges, which contain diverse communities of microorganisms including marine Actinobacteria. These exotic ecosystems may cradle rare actinomycetes with high potential to produce novel secondary metabolites. In this study, we harvested 12 different species of sponges from two locations in the Persian Gulf and isolated 45 symbiotic actinomycetes to assess their biodiversity and sponge-microbe relationships. The isolates were classified into Nocardiopsis (24 isolates), Streptomyces (17 isolates) and rare genera (4 isolates) by 16S rRNA sequencing. Antibiotic activity tests revealed that culture extracts from half of the isolates displayed growth inhibitory effects against seven pathogenic bacteria. Next, we identified five strains with the genetic potential to produce aromatic polyketides by genotyping ketosynthase genes responsible for synthesis of carbon scaffolds. The combined data led us to focus on Streptomonospora sp. PA3, since the genus has rarely been examined for its capacity to produce secondary metabolites. Analysis of culture extracts led to the discovery of a new bioactive aromatic polyketide denoted persiamycin A and 1-hydroxy-4-methoxy-2-naphthoic acid. The genome harbored seven gene clusters involved in secondary metabolism, including a tetracenomycin-type polyketide synthase pathway likely involved in persiamycin formation. The work demonstrates the use of multivariate data and underexplored ecological niches to guide the drug discovery process for antibiotics and anticancer agents.
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Affiliation(s)
- Soheila Matroodi
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Vilja Siitonen
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Bikash Baral
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Keith Yamada
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Amir Akhgari
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Mikko Metsä-Ketelä
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
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16
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Stuart KA, Welsh K, Walker MC, Edrada-Ebel R. Metabolomic tools used in marine natural product drug discovery. Expert Opin Drug Discov 2020; 15:499-522. [PMID: 32026730 DOI: 10.1080/17460441.2020.1722636] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: The marine environment is a very promising resource for natural product research, with many of these reaching the market as new drugs, especially in the field of cancer therapy as well as the drug discovery pipeline for new antimicrobials. Exploitation for bioactive marine compounds with unique structures and novel bioactivity such as the isoquinoline alkaloid; trabectedin, the polyether macrolide; halichondrin B, and the peptide; dolastatin 10, requires the use of analytical techniques, which can generate unbiased, quantitative, and qualitative data to benefit the biodiscovery process. Metabolomics has shown to bridge this understanding and facilitate the development of new potential drugs from marine sources and particularly their microbial symbionts.Areas covered: In this review, articles on applied secondary metabolomics ranging from 1990-2018 as well as to the last quarter of 2019 were probed to investigate the impact of metabolomics on drug discovery for new antibiotics and cancer treatment.Expert opinion: The current literature review highlighted the effectiveness of metabolomics in the study of targeting biologically active secondary metabolites from marine sources for optimized discovery of potential new natural products to be made accessible to a R&D pipeline.
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Affiliation(s)
- Kevin Andrew Stuart
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Keira Welsh
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Molly Clare Walker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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17
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Avalos M, Garbeva P, Raaijmakers JM, van Wezel GP. Production of ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces species. ISME JOURNAL 2019; 14:569-583. [PMID: 31700119 DOI: 10.1038/s41396-019-0537-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Soil-inhabiting streptomycetes are nature's medicine makers, producing over half of all known antibiotics and many other bioactive natural products. However, these bacteria also produce many volatiles, molecules that disperse through the soil matrix and may impact other (micro)organisms from a distance. Here, we show that soil- and surface-grown streptomycetes have the ability to kill bacteria over long distances via air-borne antibiosis. Our research shows that streptomycetes do so by producing surprisingly high amounts of the low-cost volatile ammonia, dispersing over long distances to inhibit the growth of Gram-positive and Gram-negative bacteria. Glycine is required as precursor to produce ammonia, and inactivation of the glycine cleavage system nullified ammonia biosynthesis and concomitantly air-borne antibiosis. Reduced expression of the porin master regulator OmpR and its cognate kinase EnvZ is used as a resistance strategy by E. coli cells to survive ammonia-mediated antibiosis. Finally, ammonia was shown to enhance the activity of canonical antibiotics, suggesting that streptomycetes adopt a low-cost strategy to sensitize competitors for antibiosis from a distance.
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Affiliation(s)
- Mariana Avalos
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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18
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Sinha R, Sharma B, Dangi AK, Shukla P. Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development. World J Microbiol Biotechnol 2019; 35:166. [DOI: 10.1007/s11274-019-2746-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/13/2019] [Indexed: 02/08/2023]
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19
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Identification of Cyanobacterial Strains with Potential for the Treatment of Obesity-Related Co-Morbidities by Bioactivity, Toxicity Evaluation and Metabolite Profiling. Mar Drugs 2019; 17:md17050280. [PMID: 31083362 PMCID: PMC6562398 DOI: 10.3390/md17050280] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity is a complex disease resulting in several metabolic co-morbidities and is increasing at epidemic rates. The marine environment is an interesting resource of novel compounds and in particular cyanobacteria are well known for their capacity to produce novel secondary metabolites. In this work, we explored the potential of cyanobacteria for the production of compounds with relevant activities towards metabolic diseases using a blend of target-based, phenotypic and zebrafish assays as whole small animal models. A total of 46 cyanobacterial strains were grown and biomass fractionated, yielding in total 263 fractions. Bioactivities related to metabolic function were tested in different in vitro and in vivo models. Studying adipogenic and thermogenic gene expression in brown adipocytes, lipid metabolism and glucose uptake in hepatocytes, as well as lipid metabolism in zebrafish larvae, we identified 66 (25%) active fractions. This together with metabolite profiling and the evaluation of toxicity allowed the identification of 18 (7%) fractions with promising bioactivity towards different aspects of metabolic disease. Among those, we identified several known compounds, such as eryloside T, leptosin F, pheophorbide A, phaeophytin A, chlorophyll A, present as minor peaks. Those compounds were previously not described to have bioactivities in metabolic regulation, and both known or unknown compounds could be responsible for such effects. In summary, we find that cyanobacteria hold a huge repertoire of molecules with specific bioactivities towards metabolic diseases, which needs to be explored in the future.
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20
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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21
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Machushynets NV, Wu C, Elsayed SS, Hankemeier T, van Wezel GP. Discovery of novel glycerolated quinazolinones from Streptomyces sp. MBT27. J Ind Microbiol Biotechnol 2019; 46:483-492. [PMID: 30729343 PMCID: PMC6403205 DOI: 10.1007/s10295-019-02140-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022]
Abstract
Actinobacteria are a major source of novel bioactive natural products. A challenge in the screening of these microorganisms lies in finding the favorable growth conditions for secondary metabolite production and dereplication of known molecules. Here, we report that Streptomyces sp. MBT27 produces 4-quinazolinone alkaloids in response to elevated levels of glycerol, whereby quinazolinones A (1) and B (2) form a new sub-class of this interesting family of natural products. Global Natural Product Social molecular networking (GNPS) resulted in a quinazolinone-related network that included anthranilic acid (3), anthranilamide (4), 4(3H)-quinazolinone (5), and 2,2-dimethyl-1,2-dihydroquinazolin-4(3H)-one (6). Actinomycins D (7) and X2 (8) were also identified in the extracts of Streptomyces sp. MBT27. The induction of quinazolinone production by glycerol combined with biosynthetic insights provide evidence that glycerol is integrated into the chemical scaffold. The unprecedented 1,4-dioxepane ring, that is spiro-fused into the quinazolinone backbone, is most likely formed by intermolecular etherification of two units of glycerol. Our work underlines the importance of varying the growth conditions for the discovery of novel natural products and for understanding their biosynthesis.
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Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. .,State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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22
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Du C, van Wezel GP. Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline. Proteomics 2018; 18:e1700332. [PMID: 29708658 PMCID: PMC6175363 DOI: 10.1002/pmic.201700332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Indexed: 12/23/2022]
Abstract
Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics-based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity-based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, the opportunities and challenges in microbial NP research are discussed, and, in particular, the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Affiliation(s)
- Chao Du
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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23
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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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24
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Azzollini A, Boggia L, Boccard J, Sgorbini B, Lecoultre N, Allard PM, Rubiolo P, Rudaz S, Gindro K, Bicchi C, Wolfender JL. Dynamics of Metabolite Induction in Fungal Co-cultures by Metabolomics at Both Volatile and Non-volatile Levels. Front Microbiol 2018; 9:72. [PMID: 29459851 PMCID: PMC5807337 DOI: 10.3389/fmicb.2018.00072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 11/24/2022] Open
Abstract
Fungal co-cultivation has emerged as a promising way for activating cryptic biosynthetic pathways and discovering novel antimicrobial metabolites. For the success of such studies, a key element remains the development of standardized co-cultivation methods compatible with high-throughput analytical procedures. To efficiently highlight induction processes, it is crucial to acquire a holistic view of intermicrobial communication at the molecular level. To tackle this issue, a strategy was developed based on the miniaturization of fungal cultures that allows for a concomitant survey of induction phenomena in volatile and non-volatile metabolomes. Fungi were directly grown in vials, and each sample was profiled by head space solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS), while the corresponding solid culture medium was analyzed by liquid chromatography high resolution mass spectrometry (LC-HRMS) after solvent extraction. This strategy was implemented for the screening of volatile and non-volatile metabolite inductions in an ecologically relevant fungal co-culture of Eutypa lata (Pers.) Tul. & C. Tul. (Diatrypaceae) and Botryosphaeria obtusa (Schwein.) Shoemaker (Botryosphaeriaceae), two wood-decaying fungi interacting in the context of esca disease of grapevine. For a comprehensive evaluation of the results, a multivariate data analysis combining Analysis of Variance and Partial Least Squares approaches, namely AMOPLS, was used to explore the complex LC-HRMS and GC-MS datasets and highlight dynamically induced compounds. A time-series study was carried out over 9 days, showing characteristic metabolite induction patterns in both volatile and non-volatile dimensions. Relevant links between the dynamics of expression of specific metabolite production were observed. In addition, the antifungal activity of 2-nonanone, a metabolite incrementally produced over time in the volatile fraction, was assessed against Eutypa lata and Botryosphaeria obtusa in an adapted bioassay set for volatile compounds. This compound has shown antifungal activity on both fungi and was found to be co-expressed with a known antifungal compound, O-methylmellein, induced in solid media. This strategy could help elucidate microbial inter- and intra-species cross-talk at various levels. Moreover, it supports the study of concerted defense/communication mechanisms for efficiently identifying original antimicrobials.
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Affiliation(s)
- Antonio Azzollini
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Lorenzo Boggia
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Julien Boccard
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Barbara Sgorbini
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Nicole Lecoultre
- Plant Protection, Mycology and Biotechnology, Agroscope, Nyon, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Patrizia Rubiolo
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Serge Rudaz
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Katia Gindro
- Plant Protection, Mycology and Biotechnology, Agroscope, Nyon, Switzerland
| | - Carlo Bicchi
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
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25
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van der Meij A, Willemse J, Schneijderberg MA, Geurts R, Raaijmakers JM, van Wezel GP. Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity. Antonie van Leeuwenhoek 2018; 111:679-690. [PMID: 29335919 PMCID: PMC5913384 DOI: 10.1007/s10482-018-1014-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/03/2018] [Indexed: 01/22/2023]
Abstract
Many actinobacteria live in close association with eukaryotes such as fungi, insects, animals and plants. Plant-associated actinobacteria display (endo)symbiotic, saprophytic or pathogenic life styles, and can make up a substantial part of the endophytic community. Here, we characterised endophytic actinobacteria isolated from root tissue of Arabidopsis thaliana (Arabidopsis) plants grown in soil from a natural ecosystem. Many of these actinobacteria belong to the family of Streptomycetaceae with Streptomyces olivochromogenes and Streptomyces clavifer as well represented species. When seeds of Arabidopsis were inoculated with spores of Streptomyces strain coa1, which shows high similarity to S. olivochromogenes, roots were colonised intercellularly and, unexpectedly, also intracellularly. Subsequent exposure of endophytic isolates to plant hormones typically found in root and shoot tissues of Arabidopsis led to altered antibiotic production against Escherichia coli and Bacillus subtilis. Taken together, our work reveals remarkable colonization patterns of endophytic streptomycetes with specific traits that may allow a competitive advantage inside root tissue.
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Affiliation(s)
- Anne van der Meij
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | | | - René Geurts
- Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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26
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Gomes NG, Pereira DM, Valentão P, Andrade PB. Hybrid MS/NMR methods on the prioritization of natural products: Applications in drug discovery. J Pharm Biomed Anal 2018; 147:234-249. [DOI: 10.1016/j.jpba.2017.07.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/17/2022]
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Gubbens J, Wu C, Zhu H, Filippov DV, Florea BI, Rigali S, Overkleeft HS, van Wezel GP. Intertwined Precursor Supply during Biosynthesis of the Catecholate-Hydroxamate Siderophores Qinichelins in Streptomyces sp. MBT76. ACS Chem Biol 2017; 12:2756-2766. [PMID: 28945067 PMCID: PMC5696649 DOI: 10.1021/acschembio.7b00597] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The explosive increase in genome sequencing and the advances in bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In particular, this has revealed that actinomycete genomes contain numerous orphan gene clusters that have the potential to specify many yet unknown bioactive specialized metabolites, representing a huge unexploited pool of chemical diversity. Here, we describe the discovery of a novel group of catecholate-hydroxamate siderophores termed qinichelins (2-5) from Streptomyces sp. MBT76. Correlation between the metabolite levels and the protein expression profiles identified the biosynthetic gene cluster (named qch) most likely responsible for qinichelin biosynthesis. The structure of the molecules was elucidated by bioinformatics, mass spectrometry, and NMR. The genome of Streptomyces sp. MBT76 contains three gene clusters for the production of catecholate-peptide siderophores, including a separate cluster for the production of a shared catecholate precursor. In addition, an operon in the qch cluster was identified for the production of the ornithine precursor for qinichelins, independent of primary metabolism. This biosynthetic complexity provides new insights into the challenges scientists face when applying synthetic biology approaches for natural product discovery.
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Affiliation(s)
- Jacob Gubbens
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Changsheng Wu
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE, Leiden, The Netherlands
| | - Hua Zhu
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I. Florea
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sébastien Rigali
- InBioS,
Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gilles P. van Wezel
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE, Leiden, The Netherlands
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Robertsen HL, Weber T, Kim HU, Lee SY. Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700465] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/20/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Helene Lunde Robertsen
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); Yuseong-gu Daejeon 306-701 Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); Yuseong-gu Daejeon 306-701 Republic of Korea
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Singh G, Katoch A, Razak M, Kitchlu S, Goswami A, Katoch M. Bioactive and biocontrol potential of endophytic fungi associated with Brugmansia aurea Lagerh. FEMS Microbiol Lett 2017; 364:4157277. [DOI: 10.1093/femsle/fnx194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022] Open
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Shi Y, Pan C, Wang K, Chen X, Wu X, Chen CTA, Wu B. Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery. Environ Microbiol 2017; 19:3606-3618. [DOI: 10.1111/1462-2920.13858] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Yutong Shi
- Ocean College; Zhejiang University; Hangzhou 310058 China
| | - Chengqian Pan
- Ocean College; Zhejiang University; Hangzhou 310058 China
| | - Kuiwu Wang
- Department of Applied Chemistry; Zhejiang Gongshang University; Hangzhou 310058 China
| | - Xuegang Chen
- Ocean College; Zhejiang University; Hangzhou 310058 China
| | - Xiaodan Wu
- Ocean College; Zhejiang University; Hangzhou 310058 China
| | - Chen-Tung Arthur Chen
- Ocean College; Zhejiang University; Hangzhou 310058 China
- Department of Oceanography; National Sun Yat-Sen University; Kaohsiung 80424 Taiwan
| | - Bin Wu
- Ocean College; Zhejiang University; Hangzhou 310058 China
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31
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Effective combined water and sideband suppression for low-speed tissue and in vivo MAS NMR. Anal Bioanal Chem 2017. [DOI: 10.1007/s00216-017-0450-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.
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Affiliation(s)
- Ben Lugtenberg
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Faina Kamilova
- Koppert Biological Systems, Veilingweg 14, PO Box 155, 2650 AD Berkel en Rodenrijs, Netherlands
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Crüsemann M, O’Neill EC, Larson CB, Melnik AV, Floros DJ, da Silva RR, Jensen PR, Dorrestein PC, Moore BS. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. JOURNAL OF NATURAL PRODUCTS 2017; 80:588-597. [PMID: 28335604 PMCID: PMC5367486 DOI: 10.1021/acs.jnatprod.6b00722] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
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Affiliation(s)
- Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ellis C. O’Neill
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Charles B. Larson
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexey V. Melnik
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dimitrios J Floros
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R. da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
- Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Paul R. Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Pieter C. Dorrestein
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bradley S. Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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New approaches to antibiotic discovery. Biotechnol Lett 2017; 39:805-817. [DOI: 10.1007/s10529-017-2311-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
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Westhoff S, van Wezel GP, Rozen DE. Distance-dependent danger responses in bacteria. Curr Opin Microbiol 2017; 36:95-101. [PMID: 28258981 DOI: 10.1016/j.mib.2017.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 12/23/2022]
Abstract
The last decade has seen a resurgence in our understanding of the diverse mechanisms that bacteria use to kill one another. We are also beginning to uncover the responses and countermeasures that bacteria use when faced with specific threats or general cues of potential danger from bacterial competitors. In this Perspective, we propose that diverse offensive and defensive responses in bacteria have evolved to offset dangers detected at different distances. Thus, while volatile organic compounds provide bacterial cells with a warning at the greatest distance, diffusible compounds like antibiotics or contact mediated killing systems, indicate a more pressing danger warranting highly-specific responses. In the competitive environments in which bacteria live, it is crucial that cells are able to detect real or potential dangers from other cells. By utilizing mechanisms of detection that can infer the distance from danger, bacteria can fine-tune aggressive interactions so that they can optimally respond to threats occurring with distinct levels of risk.
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Affiliation(s)
- Sanne Westhoff
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands.
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2300 BE Leiden, The Netherlands
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36
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Tan GY, Liu T. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria. Metab Eng 2017; 39:228-236. [DOI: 10.1016/j.ymben.2016.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022]
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37
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Stress-driven discovery of a cryptic antibiotic produced by Streptomyces sp. WU20 from Kueishantao hydrothermal vent with an integrated metabolomics strategy. Appl Microbiol Biotechnol 2016; 101:1395-1408. [DOI: 10.1007/s00253-016-7823-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/13/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022]
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38
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Dietz BM, Hajirahimkhan A, Dunlap TL, Bolton JL. Botanicals and Their Bioactive Phytochemicals for Women's Health. Pharmacol Rev 2016; 68:1026-1073. [PMID: 27677719 PMCID: PMC5050441 DOI: 10.1124/pr.115.010843] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Botanical dietary supplements are increasingly popular for women's health, particularly for older women. The specific botanicals women take vary as a function of age. Younger women will use botanicals for urinary tract infections, especially Vaccinium macrocarpon (cranberry), where there is evidence for efficacy. Botanical dietary supplements for premenstrual syndrome (PMS) are less commonly used, and rigorous clinical trials have not been done. Some examples include Vitex agnus-castus (chasteberry), Angelica sinensis (dong quai), Viburnum opulus/prunifolium (cramp bark and black haw), and Zingiber officinale (ginger). Pregnant women have also used ginger for relief from nausea. Natural galactagogues for lactating women include Trigonella foenum-graecum (fenugreek) and Silybum marianum (milk thistle); however, rigorous safety and efficacy studies are lacking. Older women suffering menopausal symptoms are increasingly likely to use botanicals, especially since the Women's Health Initiative showed an increased risk for breast cancer associated with traditional hormone therapy. Serotonergic mechanisms similar to antidepressants have been proposed for Actaea/Cimicifuga racemosa (black cohosh) and Valeriana officinalis (valerian). Plant extracts with estrogenic activities for menopausal symptom relief include Glycine max (soy), Trifolium pratense (red clover), Pueraria lobata (kudzu), Humulus lupulus (hops), Glycyrrhiza species (licorice), Rheum rhaponticum (rhubarb), Vitex agnus-castus (chasteberry), Linum usitatissimum (flaxseed), Epimedium species (herba Epimedii, horny goat weed), and Medicago sativa (alfalfa). Some of the estrogenic botanicals have also been shown to have protective effects against osteoporosis. Several of these botanicals could have additional breast cancer preventive effects linked to hormonal, chemical, inflammatory, and/or epigenetic pathways. Finally, although botanicals are perceived as natural safe remedies, it is important for women and their healthcare providers to realize that they have not been rigorously tested for potential toxic effects and/or drug/botanical interactions. Understanding the mechanism of action of these supplements used for women's health will ultimately lead to standardized botanical products with higher efficacy, safety, and chemopreventive properties.
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Affiliation(s)
- Birgit M Dietz
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Atieh Hajirahimkhan
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Tareisha L Dunlap
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Judy L Bolton
- University of Illinois at Chicago/National Institutes of Health Center for Botanical Dietary Supplements, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
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Beuzer P, Axelrod J, Trzoss L, Fenical W, Dasari R, Evidente A, Kornienko A, Cang H, La Clair JJ. Single dish gradient screening of small molecule localization. Org Biomol Chem 2016; 14:8241-5. [PMID: 27530345 PMCID: PMC5284121 DOI: 10.1039/c6ob01418f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Understanding trafficking in cells and tissues is one of the most critical steps in exploring the mechanisms and modes of action (MOAs) of a small molecule. Typically, deciphering the role of concentration presents one of the most difficult challenges associated with this task. Herein, we present a practical solution to this problem by developing concentration gradients within single dishes of cells. We demonstrate the method by evaluating fluorescently-labelled probes developed from two classes of natural products that have been identified as potential anti-cancer leads by STORM super-resolution microscopy.
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Affiliation(s)
- Paolo Beuzer
- The Salk Institute for Biological Sciences, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA.
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40
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Lugtenberg BJJ, Caradus JR, Johnson LJ. Fungal endophytes for sustainable crop production. FEMS Microbiol Ecol 2016; 92:fiw194. [PMID: 27624083 DOI: 10.1093/femsec/fiw194] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 11/12/2022] Open
Abstract
This minireview highlights the importance of endophytic fungi for sustainable agriculture and horticulture production. Fungal endophytes play a key role in habitat adaptation of plants resulting in improved plant performance and plant protection against biotic and abiotic stresses. They encode a vast variety of novel secondary metabolites including volatile organic compounds. In addition to protecting plants against pathogens and pests, selected fungal endophytes have been used to remove animal toxicities associated with fungal endophytes in temperate grasses, to create corn and rice plants that are tolerant to a range of biotic and abiotic stresses, and for improved management of post-harvest control. We argue that practices used in plant breeding, seed treatments and agriculture, often caused by poor knowledge of the importance of fungal endophytes, are among the reasons for the loss of fungal endophyte diversity in domesticated plants and also accounts for the reduced effectiveness of some endophyte strains to confer plant benefits. We provide recommendations on how to mitigate against these negative impacts in modern agriculture.
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Affiliation(s)
- Ben J J Lugtenberg
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - John R Caradus
- Grasslanz Technology Limited, PB 11008, Palmerston North, 4442, New Zealand
| | - Linda J Johnson
- Forage Science, AgResearch Limited, PB 11008, Palmerston North, 4442, New Zealand
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41
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Mobarhan YL, Fortier-McGill B, Soong R, Maas WE, Fey M, Monette M, Stronks HJ, Schmidt S, Heumann H, Norwood W, Simpson AJ. Comprehensive multiphase NMR applied to a living organism. Chem Sci 2016; 7:4856-4866. [PMID: 30155133 PMCID: PMC6016732 DOI: 10.1039/c6sc00329j] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/17/2016] [Indexed: 12/23/2022] Open
Abstract
Comprehensive multiphase (CMP) NMR is a novel technology that integrates all the hardware from solution-, gel- and solid-state into a single NMR probe, permitting all phases to be studied in intact samples. Here comprehensive multiphase (CMP) NMR is used to study all components in a living organism for the first time. This work describes 4 new scientific accomplishments summarized as: (1) CMP-NMR is applied to a living animal, (2) an effective method to deliver oxygen to the organisms is described which permits longer studies essential for in-depth NMR analysis in general, (3) a range of spectral editing approaches are applied to fully differentiate the various phases solutions (metabolites) through to solids (shell) (4) 13C isotopic labelling and multidimensional NMR are combined to provide detailed assignment of metabolites and structural components in vivo. While not explicitly studied here the multiphase capabilities of the technique offer future possibilities to study kinetic transfer between phases (e.g. nutrient assimilation, contaminant sequestration), molecular binding at interfaces (e.g. drug or contaminant binding) and bonding across and between phases (e.g. muscle to bone) in vivo. Future work will need to focus on decreasing the spinning speed to reduce organism stress during analysis.
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Affiliation(s)
- Yalda Liaghati Mobarhan
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Blythe Fortier-McGill
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Ronald Soong
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
| | - Werner E Maas
- Bruker BioSpin Corp. , 15 Fortune Drive , Billerica , Massachusetts , USA 01821-3991
| | - Michael Fey
- Bruker BioSpin Corp. , 15 Fortune Drive , Billerica , Massachusetts , USA 01821-3991
| | - Martine Monette
- Bruker BioSpin Canada , 555 Steeles Avenue East , Milton , ON , Canada L9T 1Y6
| | - Henry J Stronks
- Bruker BioSpin Canada , 555 Steeles Avenue East , Milton , ON , Canada L9T 1Y6
| | | | | | - Warren Norwood
- Environment Canada , 867 Lakeshore Rd. , Burlington , ON , Canada L7R 4A6
| | - André J Simpson
- Department of Physical and Environmental Science , University of Toronto , 1265 Military Trail , Toronto , ON , Canada M1C 1A4 .
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42
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Frédérich M, Pirotte B, Fillet M, de Tullio P. Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine. J Med Chem 2016; 59:8649-8666. [PMID: 27295417 DOI: 10.1021/acs.jmedchem.5b01335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
"Omics" sciences have been developed to provide a holistic point of view of biology and to better understand the complexity of an organism as a whole. These systems biology approaches can be examined at different levels, starting from the most fundamental, i.e., the genome, and finishing with the most functional, i.e., the metabolome. Similar to how genomics is applied to the exploration of DNA, metabolomics is the qualitative and quantitative study of metabolites. This emerging field is clearly linked to genomics, transcriptomics, and proteomics. In addition, metabolomics provides a unique and direct vision of the functional outcome of an organism's activities that are required for it to survive, grow, and respond to internal and external stimuli or stress, e.g., pathologies and drugs. The links between metabolic changes, patient phenotype, physiological and/or pathological status, and treatment are now well established and have opened a new area for the application of metabolomics in the drug discovery process and in personalized medicine.
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Affiliation(s)
- Michel Frédérich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Pascal de Tullio
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
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Olsen EK, Søderholm KL, Isaksson J, Andersen JH, Hansen E. Metabolomic Profiling Reveals the N-Acyl-Taurine Geodiataurine in Extracts from the Marine Sponge Geodia macandrewii (Bowerbank). JOURNAL OF NATURAL PRODUCTS 2016; 79:1285-1291. [PMID: 27100857 DOI: 10.1021/acs.jnatprod.5b00966] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A metabolomic approach was used to identify known and new natural products from the marine sponges Geodia baretti and G. macandrewii. G. baretti is known to produce bioactive natural products such as barettin (1), 8,9-dihydrobarettin (2), and bromobenzisoxazolone barettin (3), while secondary metabolites from G. macandrewii are not reported in the literature. Specimens of the two sponges were collected from different sites along the coast of Norway, and their extracts were analyzed using UHPLC-HR-MS. Metabolomic analyses revealed that extracts from both species contained barettin (1) and 8,9-dihydrobarettin (2), and all samples of G. baretti contained higher amounts of both compounds compared to G. macandrewii. The analysis of the MS data also revealed that samples of G. macandrewii contained a compound that was not present in any of the G. baretti samples. This new compound was isolated and identified as the N-acyl-taurine geodiataurine (4), and it was tested for antioxidant, anticancer, and antibacterial properties.
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Affiliation(s)
- Elisabeth K Olsen
- MabCent-SFI, ‡Department of Chemistry, and §Marbio, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Kine L Søderholm
- MabCent-SFI, ‡Department of Chemistry, and §Marbio, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Johan Isaksson
- MabCent-SFI, ‡Department of Chemistry, and §Marbio, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Jeanette H Andersen
- MabCent-SFI, ‡Department of Chemistry, and §Marbio, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
| | - Espen Hansen
- MabCent-SFI, ‡Department of Chemistry, and §Marbio, UiT The Arctic University of Norway , N-9037 Tromsø, Norway
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Jia X, Liu C, Song H, Ding M, Du J, Ma Q, Yuan Y. Design, analysis and application of synthetic microbial consortia. Synth Syst Biotechnol 2016; 1:109-117. [PMID: 29062933 PMCID: PMC5640696 DOI: 10.1016/j.synbio.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.
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Affiliation(s)
- Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Chang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Qian Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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Weber T, Kim HU. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. Synth Syst Biotechnol 2016; 1:69-79. [PMID: 29062930 PMCID: PMC5640684 DOI: 10.1016/j.synbio.2015.12.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/10/2015] [Accepted: 12/26/2015] [Indexed: 01/02/2023] Open
Abstract
Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work. In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.
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Key Words
- A, adenylation domain
- Antibiotics
- BGC, biosynthetic gene cluster
- Bioinformatics
- Biosynthesis
- C, condensation domain
- GPR, gene-protein-reaction
- HMM, hidden Markov model
- LC, liquid chromatography
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- NRP, non-ribosomally synthesized peptide
- NRPS
- NRPS, non-ribosomal peptide synthetase
- Natural product
- PCP, peptidyl carrier protein
- PK, polyketide
- PKS
- PKS, polyketide synthase
- RiPP, ribosomally and post-translationally modified peptide
- SVM, support vector machine
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Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark.,BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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46
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Wu C, Zhu H, van Wezel GP, Choi YH. Metabolomics-guided analysis of isocoumarin production by Streptomyces species MBT76 and biotransformation of flavonoids and phenylpropanoids. Metabolomics 2016; 12:90. [PMID: 27073352 PMCID: PMC4819732 DOI: 10.1007/s11306-016-1025-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/18/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Actinomycetes produce the majority of the antibiotics currently in clinical use. The efficiency of antibiotic production is affected by multiple factors such as nutrients, pH, temperature and growth phase. Finding the optimal harvesting time is crucial for successful isolation of the desired bioactive metabolites from actinomycetes, but for this conventional chemical analysis has limitations due to the metabolic complexity. OBJECTIVES This study explores the utility of NMR-based metabolomics for (1) optimizing fermentation time for the production of known and/or unknown bioactive compounds produced by actinomycetes; (2) elucidating the biosynthetic pathway for microbial natural products; and (3) facilitating the biotransformation of nature-abundant chemicals. METHOD The aqueous culture broth of actinomycete Streptomyces sp. MBT76 was harvested every 24 h for 5 days and each broth was extracted by ethyl acetate. The extracts were analyzed by 1H NMR spectroscopy and the data were compared with principal component analysis (PCA) and orthogonal projection to latent structures (OPLS) analysis. Antimicrobial test were performed by agar diffusion assay. RESULTS The secondary metabolites production by Streptomyces sp. MBT76 was growth phase-dependent. Isocoumarins (1-9), undecylprodiginine (10), streptorubin B (11), 1H-pyrrole-2-carboxamide (12), acetyltryptamine (13), and fervenulin (14) were identified, and their optimal production time was determined in crude extracts without tedious chromatographic fractionation. Of these compounds, 5,6,7,8-tetramethoxyl-3-methyl-isocoumarin (9) is as a novel compound, which was most likely synthesized by a type I iterative polyketide synthase (PKS) encoded by the icm gene cluster. Multivariate data analysis of the 1H NMR spectra showed that acetyltryptamine (13) and tri-methoxylated isocoumarins (7 and 8) were the major determinants of antibiotic activity during later time points. The methoxylation was exploited to allow bioconversion of exogenously added genistein into a suite of methoxylated isoflavones (15-18). Methoxylation increased the antimicrobial efficacy of isocoumarins, but decreased that of the isoflavones. CONCLUSION Our results show the applicability of NMR-based metabolic profiling to streamline microbial biotransformation and to determine the optimal harvesting time of actinomycetes for antibiotic production.
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Affiliation(s)
- Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Hua Zhu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg, 72, 2333 BE Leiden, The Netherlands
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Wu C, Du C, Gubbens J, Choi YH, van Wezel GP. Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by Streptomyces Species MBT28. JOURNAL OF NATURAL PRODUCTS 2015; 78:2355-2363. [PMID: 26438963 DOI: 10.1021/acs.jnatprod.5b00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by Streptomyces sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (1) with antimicrobial activity against Bacillus subtilis. The metabolite-guided genome mining of Streptomyces sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics.
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Affiliation(s)
| | | | - Jacob Gubbens
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Mittermeier VK, Schmitt N, Volk LPM, Suárez JP, Beck A, Eisenreich W. Metabolic Profiling of Alpine and Ecuadorian Lichens. Molecules 2015; 20:18047-65. [PMID: 26437395 PMCID: PMC6332210 DOI: 10.3390/molecules201018047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 01/29/2023] Open
Abstract
Non-targeted ¹H-NMR methods were used to determine metabolite profiles from crude extracts of Alpine and Ecuadorian lichens collected from their natural habitats. In control experiments, the robustness of metabolite detection and quantification was estimated using replicate measurements of Stereocaulon alpinum extracts. The deviations in the overall metabolite fingerprints were low when analyzing S. alpinum collections from different locations or during different annual and seasonal periods. In contrast, metabolite profiles observed from extracts of different Alpine and Ecuadorian lichens clearly revealed genus- and species-specific profiles. The discriminating functions determining cluster formation in principle component analysis (PCA) were due to differences in the amounts of genus-specific compounds such as sticticin from the Sticta species, but also in the amounts of ubiquitous metabolites, such as sugar alcohols or trehalose. However, varying concentrations of these metabolites from the same lichen species e.g., due to different environmental conditions appeared of minor relevance for the overall cluster formation in PCA. The metabolic clusters matched phylogenetic analyses using nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences of lichen mycobionts, as exemplified for the genus Sticta. It can be concluded that NMR-based non-targeted metabolic profiling is a useful tool in the chemo-taxonomy of lichens. The same approach could also facilitate the discovery of novel lichen metabolites on a rapid and systematical basis.
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Affiliation(s)
- Verena K Mittermeier
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenberg-Str. 4, D-85747 Garching, Germany.
| | - Nicola Schmitt
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenberg-Str. 4, D-85747 Garching, Germany.
| | - Lukas P M Volk
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenberg-Str. 4, D-85747 Garching, Germany.
| | - Juan Pablo Suárez
- Departamento de Ciencias Naturales, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, C.P. 11 01 608 Loja, Ecuador.
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, Menzinger Str. 67, D-80638 München, Germany.
- GeoBio-Center, Ludwig-Maximilians Universität München, Richard-Wagner-Str. 10, D-80333 München, Germany.
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenberg-Str. 4, D-85747 Garching, Germany.
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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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50
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Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation. Sci Rep 2015; 5:10868. [PMID: 26040782 PMCID: PMC4455117 DOI: 10.1038/srep10868] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/29/2015] [Indexed: 12/20/2022] Open
Abstract
Actinomycetes and filamentous fungi produce a wide range of bioactive compounds, with applications as antimicrobials, anticancer agents or agrochemicals. Their genomes contain a far larger number of gene clusters for natural products than originally anticipated, and novel approaches are required to exploit this potential reservoir of new drugs. Here, we show that co-cultivation of the filamentous model microbes Streptomyces coelicolor and Aspergillus niger has a major impact on their secondary metabolism. NMR-based metabolomics combined with multivariate data analysis revealed several compounds that correlated specifically to co-cultures, including the cyclic dipeptide cyclo(Phe-Phe) and 2-hydroxyphenylacetic acid, both of which were produced by A. niger in response to S. coelicolor. Furthermore, biotransformation studies with o-coumaric acid and caffeic acid resulted in the production of the novel compounds (E)-2-(3-hydroxyprop-1-en-1-yl)-phenol and (2E,4E)-3-(2-carboxy-1-hydroxyethyl)-2,4-hexadienedioxic acid, respectively. This highlights the utility of microbial co-cultivation combined with NMR-based metabolomics as an efficient pipeline for the discovery of novel natural products.
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