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Parra J, Jarmusch SA, Duncan KR. Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems. Environ Microbiol 2024; 26:e16635. [PMID: 38899724 DOI: 10.1111/1462-2920.16635] [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: 08/02/2023] [Accepted: 04/25/2024] [Indexed: 06/21/2024]
Abstract
Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.
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Affiliation(s)
- Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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2
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Rill A, Zhao L, Bode HB. Genetic toolbox for Photorhabdus and Xenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling. Microb Cell Fact 2024; 23:98. [PMID: 38561780 PMCID: PMC10983751 DOI: 10.1186/s12934-024-02363-8] [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: 12/17/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bacteria of the genus Photorhabdus and Xenorhabdus are motile, Gram-negative bacteria that live in symbiosis with entomopathogenic nematodes. Due to their complex life cycle, they produce a large number of specialized metabolites (natural products) encoded in biosynthetic gene clusters (BGC). Genetic tools for Photorhabdus and Xenorhabdus have been rare and applicable to only a few strains. In the past, several tools have been developed for the activation of BGCs and the deletion of individual genes. However, these often have limited efficiency or are time consuming. Among the limitations, it is essential to have versatile expression systems and genome editing tools that could facilitate the practical work. RESULTS In the present study, we developed several expression vectors and a CRISPR-Cpf1 genome editing vector for genetic manipulations in Photorhabdus and Xenorhabdus using SEVA plasmids. The SEVA collection is based on modular vectors that allow exchangeability of different elements (e.g. origin of replication and antibiotic selection markers with the ability to insert desired sequences for different end applications). Initially, we tested different SEVA vectors containing the broad host range origins and three different resistance genes for kanamycin, gentamycin and chloramphenicol, respectively. We demonstrated that these vectors are replicative not only in well-known representatives, e.g. Photorhabdus laumondii TTO1, but also in other rarely described strains like Xenorhabdus sp. TS4. For our CRISPR/Cpf1-based system, we used the pSEVA231 backbone to delete not only small genes but also large parts of BGCs. Furthermore, we were able to activate and refactor BGCs to obtain high production titers of high value compounds such as safracin B, a semisynthetic precursor for the anti-cancer drug ET-743. CONCLUSIONS The results of this study provide new inducible expression vectors and a CRISPR/CPf1 encoding vector all based on the SEVA (Standard European Vector Architecture) collection, which can improve genetic manipulation and genome editing processes in Photorhabdus and Xenorhabdus.
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Affiliation(s)
- Alexander Rill
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043, Marburg, Germany.
- Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.
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3
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [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: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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4
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Meng Z, Tan Y, Duan YL, Li M. Monaspin B, a Novel Cyclohexyl-furan from Cocultivation of Monascus purpureus and Aspergillus oryzae, Exhibits Potent Antileukemic Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1114-1123. [PMID: 38166364 DOI: 10.1021/acs.jafc.3c08187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Natural products are a rich resource for the discovery of innovative drugs. Microbial cocultivation enables discovery of novel natural products through tandem enzymatic catalysis between different fungi. In this study, Monascus purpureus, as a food fermentation strain capable of producing abundant natural products, was chosen as an example of a cocultivation pair strain. Cocultivation screening revealed that M. purpureus and Aspergillus oryzae led to the production of two novel cyclohexyl-furans, Monaspins A and B. Optimization of the cocultivation mode and media enhanced the production of Monaspins A and B to 1.2 and 0.8 mg/L, respectively. Monaspins A and B were structurally elucidated by HR-ESI-MS and NMR. Furthermore, Monaspin B displayed potent antiproliferative activity against the leukemic HL-60 cell line by inducing apoptosis, with a half-maximal inhibitory concentration (IC50) of 160 nM. Moreover, in a mouse leukemia model, Monaspin B exhibited a promising in vivo antileukemic effect by reducing white blood cell, lymphocyte, and neutrophil counts. Collectively, these results indicate that Monaspin B is a promising candidate agent for leukemia therapy.
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Affiliation(s)
- Zitong Meng
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, Tongji Medical College, Huazhong University of Science and Technology, Hangkong Road 13, Wuhan 430030, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Ya-Li Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
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5
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Lee YCJ, Javdan B. Ice Cores as a Source for Antimicrobials: From Bioprospecting to Biodesign. BIODESIGN RESEARCH 2023; 5:0024. [PMID: 37928441 PMCID: PMC10623340 DOI: 10.34133/bdr.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023] Open
Abstract
The golden age has passed for antibiotic discovery, and while some antibiotics are currently in various phases of clinical trials in the United States, many pharmaceutical companies have abandoned antibiotic research. With the need for antibiotics, we should expand our horizon for therapeutic mining and can look toward understudied sources such as ice cores. Ice cores contain microorganisms and genetic material that have been frozen in time for thousands of years. The antibiotics used by these organisms are encoded in their genomes, which can be unlocked, identified, and characterized with modern advances in molecular biology, genetic sequencing, various computational approaches, and established natural product discovery pipelines. While synthetic biology can be used in natural product discovery approaches, synthetic biology and bioengineering efforts can also be leveraged in the selection and biodesign of increased compound yields, potency, and stability. Here, we provide the perspective that ice cores can be a source of novel antibiotic compounds and that the tools of synthetic biology can be used to design better antimicrobials.
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Affiliation(s)
| | - Bahar Javdan
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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6
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Gómez-Pérez D, Schmid M, Chaudhry V, Hu Y, Velic A, Maček B, Ruhe J, Kemen A, Kemen E. Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria. THE NEW PHYTOLOGIST 2023; 239:2320-2334. [PMID: 37222268 DOI: 10.1111/nph.18995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo-colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram-positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.
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Affiliation(s)
- Daniel Gómez-Pérez
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Monja Schmid
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Vasvi Chaudhry
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Yiheng Hu
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Ana Velic
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Boris Maček
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Jonas Ruhe
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ariane Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
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7
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Du L, Haldar S, King JB, Mattes AO, Srivastava S, Wendt KL, You J, Cunningham C, Cichewicz RH. Persephacin Is a Broad-Spectrum Antifungal Aureobasidin Metabolite That Overcomes Intrinsic Resistance in Aspergillus fumigatus. JOURNAL OF NATURAL PRODUCTS 2023; 86:1980-1993. [PMID: 37523665 DOI: 10.1021/acs.jnatprod.3c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Fungi pose a persistent threat to humankind with worrying indications that emerging and re-emerging pathogens (e.g., Candida auris, Coccidioides spp., drug-resistant Aspergilli, and more) exhibit resistance to the limited number of approved antifungals. To address this problem, our team is exploring endophytic fungi as a resource for the discovery of new antifungal natural products. The rationale behind this decision is based on evidence that endophytes engage with plants in mutualistic relationships wherein some fungi actively participate by producing chemical defense measures that suppress pathogenic microorganisms. To improve the odds of bioactive metabolite discovery, we developed a new hands-free laser-cutting system capable of generating >50 plant samples per minute that, in turn, enabled our team to prepare and screen large numbers of endophytic fungi. One of the fungal isolates obtained in this way was identified as an Elsinoë sp. that produced a unique aureobasidin analogue, persephacin (1). Some distinctive features of 1 are the absence of both phenylalanine residues combined with the incorporation of a novel amino acid residue, persephanine (9). Compound 1 exhibits potent antifungal effects against a large number of pathogenic yeast (including several clinical C. auris strains), as well as phylogenetically diverse filamentous fungi (e.g., Aspergillus fumigatus). In an ex vivo eye infection model, compound 1 outperformed standard-of-care treatments demonstrating the ability to suppress fluconazole-resistant Candida albicans and A. fumigatus at a concentration (0.1% solution) well below the clinically recommended levels used for fluconazole and natamycin (2% and 5% solutions, respectively). In 3D tissue models for acute dermal and ocular safety, 1 was found to be nontoxic and nonirritating at concentrations required to elicit antifungal activity. Natural product 1 appears to be a promising candidate for further investigation as a broad-spectrum antifungal capable of controlling a range of pathogens that negatively impact human, animal, and plant health.
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Affiliation(s)
- Lin Du
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Saikat Haldar
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jarrod B King
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Allison O Mattes
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shikha Srivastava
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jianlan You
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Chad Cunningham
- Electronics & Instrument Shop, Department of Physics and Astronomy, Nielsen Hall, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Robert H Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
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8
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MacAlpine J, Robbins N, Cowen LE. Bacterial-fungal interactions and their impact on microbial pathogenesis. Mol Ecol 2023; 32:2565-2581. [PMID: 35231147 PMCID: PMC11032213 DOI: 10.1111/mec.16411] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 02/18/2022] [Indexed: 11/27/2022]
Abstract
Microbial communities of the human microbiota exhibit diverse effects on human health and disease. Microbial homeostasis is important for normal physiological functions and changes to the microbiota are associated with many human diseases including diabetes, cancer, and colitis. In addition, there are many microorganisms that are either commensal or acquired from environmental reservoirs that can cause diverse pathologies. Importantly, the balance between health and disease is intricately connected to how members of the microbiota interact and affect one another's growth and pathogenicity. However, the mechanisms that govern these interactions are only beginning to be understood. In this review, we outline bacterial-fungal interactions in the human body, including examining the mechanisms by which bacteria govern fungal growth and virulence, as well as how fungi regulate bacterial pathogenesis. We summarize advances in the understanding of chemical, physical, and protein-based interactions, and their role in exacerbating or impeding human disease. We focus on the three fungal species responsible for the majority of systemic fungal infections in humans: Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. We conclude by summarizing recent studies that have mined microbes for novel antimicrobials and antivirulence factors, highlighting the potential of the human microbiota as a rich resource for small molecule discovery.
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Affiliation(s)
- Jessie MacAlpine
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
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9
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Torres Salazar B, Lange A, Camus L, Heilbronner S. Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals. Methods Mol Biol 2023; 2601:39-54. [PMID: 36445578 DOI: 10.1007/978-1-0716-2855-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Soil-derived microorganisms have been sampled intensively throughout the last decades in order to discover bacterial strains that produce new antibiotics. The increasing emergence of multidrug-resistant bacteria and the constant high demand for new antibiotic classes are leading to the sampling and investigation of new microbiomes that contain antimicrobial producers. Human-associated microbiomes are therefore gaining more and more attention. This chapter presents a detailed description of how human microbiomes can be sampled and how microbiota members from skin and nasal samples can be isolated. Different methods for antimicrobial compound screening are presented.
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Affiliation(s)
- Benjamin Torres Salazar
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
| | - Anna Lange
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Laura Camus
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, Tübingen, Germany.
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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10
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Kontomina E, Garefalaki V, Fylaktakidou KC, Evmorfidou D, Eleftheraki A, Avramidou M, Udoh K, Panopoulou M, Felföldi T, Márialigeti K, Fakis G, Boukouvala S. A taxonomically representative strain collection to explore xenobiotic and secondary metabolism in bacteria. PLoS One 2022; 17:e0271125. [PMID: 35834592 PMCID: PMC9282458 DOI: 10.1371/journal.pone.0271125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/23/2022] [Indexed: 11/20/2022] Open
Abstract
Bacteria employ secondary metabolism to combat competitors, and xenobiotic metabolism to survive their chemical environment. This project has aimed to introduce a bacterial collection enabling comprehensive comparative investigations of those functions. The collection comprises 120 strains (Proteobacteria, Actinobacteria and Firmicutes), and was compiled on the basis of the broad taxonomic range of isolates and their postulated biosynthetic and/or xenobiotic detoxification capabilities. The utility of the collection was demonstrated in two ways: first, by performing 5144 co-cultures, recording inhibition between isolates and employing bioinformatics to predict biosynthetic gene clusters in sequenced genomes of species; second, by screening for xenobiotic sensitivity of isolates against 2-benzoxazolinone and 2-aminophenol. The co-culture medium of Bacillus siamensis D9 and Lysinibacillus sphaericus DSM 28T was further analysed for possible antimicrobial compounds, using liquid chromatography-mass spectrometry (LC-MS), and guided by computational predictions and the literature. Finally, LC-MS analysis demonstrated N-acetylation of 3,4-dichloroaniline (a toxic pesticide residue of concern) by the actinobacterium Tsukamurella paurometabola DSM 20162T which is highly tolerant of the xenobiotic. Microbial collections enable "pipeline" comparative screening of strains: on the one hand, bacterial co-culture is a promising approach for antibiotic discovery; on the other hand, bioremediation is effective in combating pollution, but requires knowledge of microbial xenobiotic metabolism. The presented outcomes are anticipated to pave the way for studies that may identify bacterial strains and/or metabolites of merit in biotechnological applications.
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Affiliation(s)
- Evanthia Kontomina
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vasiliki Garefalaki
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Dorothea Evmorfidou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athina Eleftheraki
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Marina Avramidou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Karen Udoh
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Panopoulou
- Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Giannoulis Fakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Sotiria Boukouvala
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- * E-mail:
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11
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Harnessing Rare Actinomycete Interactions and Intrinsic Antimicrobial Resistance Enables Discovery of an Unusual Metabolic Inhibitor. mBio 2022; 13:e0039322. [PMID: 35608300 PMCID: PMC9239090 DOI: 10.1128/mbio.00393-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products have historically been a deep source of new medicines, but their slowed discovery in recent decades has put a premium on developing strategies that enhance the likelihood of capturing novel compounds. Here, we used a straightforward approach that capitalizes on the interactive ecology of “rare” actinomycetes. Specifically, we screened for interactions that triggered the production of antimicrobials that inhibited the growth of a bacterial strain with exceptionally diverse natural antimicrobial resistance. This strategy led to the discovery of a family of antimicrobials we term the dynaplanins. Heterologous expression enabled identification of the dynaplanin biosynthetic gene cluster, which was missed by typical algorithms for natural product gene cluster detection. Genome sequencing of partially resistant mutants revealed a 2-oxo acid dehydrogenase E2 subunit as the likely molecular target of the dynaplanins, and this finding was supported by computational modeling of the dynaplanin scaffold within the active site of this enzyme. Thus, this simple strategy, which leverages microbial interactions and natural antibiotic resistance, can enable discovery of molecules with unique antimicrobial activity. In addition, these results indicate that primary metabolism may be a direct target for inhibition via chemical interference in competitive microbial interactions.
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12
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Zhai YJ, Huo GM, Wei J, Lin LB, Zhang Q, Li JN, Chen X, Han WB, Gao JM. Structures and absolute configurations of butenolide derivatives from the isopod-associated fungus Pidoplitchkoviella terricola. PHYTOCHEMISTRY 2022; 193:112981. [PMID: 34653910 DOI: 10.1016/j.phytochem.2021.112981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
In this research, twenty aromatic and branched aliphatic polyketides, including seven previously undescribed butenolide derivatives, piterriones A-G and one known analogue, along with twelve known altenusin derivatives, were isolated from the isopod-associated fungus Pidoplitchkoviella terricola. Their structures were elucidated by analysis of NMR (1D and 2D) and mass spectrometry data, and their absolute configurations were determined by Mosher's method, microscale derivatization, and comparison of their specific rotations and ECD spectra. Dihydroaltenuene B exhibited mushroom tyrosinase inhibitory activity with an IC50 value of 38.33 ± 1.59 μM, which was comparable to that of the positive control, kojic acid (IC50 = 39.72 ± 1.34 μM). A molecular-docking study disclosed the hydrogen bonding interactions between the 3-OH and 4'-OH of dihydroaltenuene B and the His244, Met280 and Gly281 residues of tyrosinase.
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Affiliation(s)
- Yi-Jie Zhai
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Guang-Ming Huo
- Institute of Medicinal Fungi, School of Food Science, Nanjing Xiaozhuang University, Nanjing, Jiangsu, 210017, People's Republic of China
| | - Jing Wei
- College of Biology Pharmacy & Food Engineering, Shangluo University, Shangluo, 726000, Shaanxi, People's Republic of China
| | - Li-Bin Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Jian-Nan Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Xin Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Wen-Bo Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.
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13
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Di Martino P. Antimicrobial agents and microbial ecology. AIMS Microbiol 2022; 8:1-4. [PMID: 35496989 PMCID: PMC8995183 DOI: 10.3934/microbiol.2022001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 11/18/2022] Open
Abstract
Antimicrobials are therapeutic substances used to prevent or treat infections. Disinfectants are antimicrobial agents applied to non-living surfaces. Every year, several thousand tonnes of antimicrobials and their by-products are released into the environment and in particular into the aquatic environment. This type of xenobiotic has ecological consequences in the natural environment but also in technological environments such as wastewater treatment plants and methane fermentation sewage sludge treatment plants. The constant exposure of microbial communities not only to high concentrations but also to sub-inhibitory concentrations of antibiotics is a key element in the development of antibiotic resistance in aquatic environments and in soils. The future of antimicrobials lies in the development of biosourced or bioinspired molecules. The observation and deciphering of interactions between living organisms is the key to this development.
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14
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Adams AE, Besozzi EM, Shahrokhi G, Patten MA. A case for associational resistance: Apparent support for the stress gradient hypothesis varies with study system. Ecol Lett 2021; 25:202-217. [PMID: 34775662 DOI: 10.1111/ele.13917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
According to the stress gradient hypothesis (SGH), ecological interactions between organisms shift positively as environmental stress increases. In the case of associational resistance, habitat is modified to ameliorate stress, benefitting other organisms. The SGH is contentious due to conflicting evidence and theoretical perspectives, so we adopted a meta-analytic approach to determine if it is widely supported across a variety of contexts, including different kingdoms, ecosystems, habitats, interactions, stressors, and life history stages. We developed an extensive list of Boolean search criteria to search the published ecological literature and successfully detect studies that both directly tested the hypothesis, and those that were relevant but never mentioned it. We found that the SGH is well supported by studies that feature bacteria, plants, terrestrial ecosystems, interspecific negative interactions, adults, survival instead of growth or reproduction, and drought, fire, and nutrient stress. We conclude that the SGH is indeed a broadly relevant ecological hypothesis that is currently held back by cross-disciplinary communication barriers. More SGH research is needed beyond the scope of interspecific plant competition, and more SGH research should feature multifactor stress. There remains a need to account for positive interactions in scientific pursuits, such as associational resistance in tests of the SGH.
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Affiliation(s)
- Amy E Adams
- Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
| | | | - Golya Shahrokhi
- Oklahoma Biological Survey, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael A Patten
- Ecology Research Group, Faculty of Biosciences and Aquaculture, Nord University, Steinkjer, Norway
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15
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Rebuffat S. Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions. Nat Prod Rep 2021; 39:273-310. [PMID: 34755755 DOI: 10.1039/d1np00052g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is currently well established that multicellular organisms live in tight association with complex communities of microorganisms including a large number of bacteria. These are immersed in complex interaction networks reflecting the relationships established between them and with host organisms; yet, little is known about the molecules and mechanisms involved in these mutual interactions. Ribosomally synthesized peptides, among which bacterial antimicrobial peptides called bacteriocins and microcins have been identified as contributing to host-microbe interplays, are either unmodified or post-translationally modified peptides. This review will unveil current knowledge on these ribosomal peptide-based natural products, their interplay with the host immune system, and their roles in microbial interactions and symbioses. It will include their major structural characteristics and post-translational modifications, the main rules of their maturation pathways, and the principal ecological functions they ensure (communication, signalization, competition), especially in symbiosis, taking select examples in various organisms. Finally, we address unanswered questions and provide a framework for deciphering big issues inspiring future directions in the field.
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Affiliation(s)
- Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), National Centre of Scientific Research (CNRS), CP 54, 57 rue Cuvier 75005, Paris, France.
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16
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Boruta T, Ścigaczewska A, Bizukojć M. "Microbial Wars" in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites. Front Bioeng Biotechnol 2021; 9:713639. [PMID: 34660550 PMCID: PMC8511322 DOI: 10.3389/fbioe.2021.713639] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial co-cultivation is an approach frequently used for the induction of secondary metabolic pathways and the discovery of novel molecules. The studies of this kind are typically focused on the chemical and ecological aspects of inter-species interactions rather than on the bioprocess characterization. In the present work, the co-cultivation of two textbook producers of secondary metabolites, namely Aspergillus terreus (a filamentous fungus used for the manufacturing of lovastatin, a cholesterol-lowering drug) and Streptomyces rimosus (an actinobacterial producer of an antibiotic oxytetracycline) in a 5.5-L stirred tank bioreactor was investigated in the context of metabolic production, utilization of carbon substrates and dissolved oxygen levels. The cultivation runs differed in terms of the applied co-culture initiation strategy and the composition of growth medium. All the experiments were performed in three bioreactors running in parallel (corresponding to a co-culture and two respective monoculture controls). The analysis based upon mass spectrometry and liquid chromatography revealed a broad spectrum of more than 40 secondary metabolites, including the molecules identified as the oxidized derivatives of rimocidin and milbemycin that were observed solely under the conditions of co-cultivation. S. rimosus showed a tendency to dominate over A. terreus, except for the runs where S. rimosus was inoculated into the already developed bioreactor cultures of A. terreus. Despite being dominated, the less aggressive strain still had an observable influence on the production of secondary metabolites and the utilization of substrates in co-culture. The monitoring of dissolved oxygen levels was evaluated as a fast approach of identifying the dominant microorganism during the co-cultivation process.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Marcin Bizukojć
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
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17
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Hussain N, Delar E, Piochon M, Groleau MC, Tebbji F, Sellam A, Déziel E, Gauthier C. Total synthesis of the proposed structures of gladiosides I and II. Carbohydr Res 2021; 507:108373. [PMID: 34157641 DOI: 10.1016/j.carres.2021.108373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Burkholderia gladioli is a Gram-negative bacterium that biosynthesizes a cocktail of potent antimicrobial compounds, including the antifungal phenolic glycoside sinapigladioside. Herein, we report the total synthesis of the proposed structures of gladiosides I and II, two structurally related phenolic glycosides previously isolated from B. gladioli OR1 cultures. Importantly, the physical and analytical data of the synthetic compounds were in significant discrepancies with the natural products suggesting a misassignment of the originally proposed structures. Furthermore, we have uncovered an acid-catalyzed fragmentation mechanism converting the α,β-unsaturated methyl carbamate-containing gladioside II into the aldehyde-containing gladioside I. Our results lay the foundation for the expeditious synthesis of derivatives of these Burkholderia-derived phenolic glycosides, which would enable to decipher their biological roles and potential pharmacological properties.
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Affiliation(s)
- Nazar Hussain
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada
| | - Emmanilo Delar
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada
| | - Marianne Piochon
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada
| | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada
| | - Faiza Tebbji
- Department of Microbiology, Infectious Disease and Immunology, Montreal Heart Institute, Université de Montréal, 5000 Rue Bélanger, Montréal (Québec), H1T 1C8, Canada
| | - Adnane Sellam
- Department of Microbiology, Infectious Disease and Immunology, Montreal Heart Institute, Université de Montréal, 5000 Rue Bélanger, Montréal (Québec), H1T 1C8, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada
| | - Charles Gauthier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), 531 Boulevard des Prairies, Laval (Québec), H7V 1B7, Canada.
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18
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Um S, Guo H, Thiengmag S, Benndorf R, Murphy R, Rischer M, Braga D, Poulsen M, de Beer ZW, Lackner G, Beemelmanns C. Comparative Genomic and Metabolic Analysis of Streptomyces sp. RB110 Morphotypes Illuminates Genomic Rearrangements and Formation of a New 46-Membered Antimicrobial Macrolide. ACS Chem Biol 2021; 16:1482-1492. [PMID: 34275291 DOI: 10.1021/acschembio.1c00357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Morphotype switches frequently occur in Actinobacteria and are often associated with disparate natural product production. Here, we report on differences in the secondary metabolomes of two morphotypes of a Streptomyces species, including the discovery of a novel antimicrobial glycosylated macrolide, which we named termidomycin A. While exhibiting an unusual 46-member polyene backbone, termidomycin A (1) shares structural features with the clinically important antifungal agents amphotericin B and nystatin A1. Genomic analyses revealed a biosynthetic gene cluster encoding for a putative giant type I polyketide synthase (PKS), whose domain structure allowed us to propose the relative configuration of the 46-member macrolide. The architecture of the biosynthetic gene cluster was different in both morphotypes, thus leading to diversification of the product spectrum. Given the high frequency of genomic rearrangements in Streptomycetes, the metabolic analysis of distinct morphotypes as exemplified in this study is a promising approach for the discovery of bioactive natural products and pathways of diversification.
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Affiliation(s)
- Soohyun Um
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Huijuan Guo
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sirinthra Thiengmag
- Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - René Benndorf
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Robert Murphy
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark
| | - Maja Rischer
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Daniel Braga
- Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen East, Denmark
| | - Z. Wilhelm de Beer
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Gerald Lackner
- Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
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19
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Leinberger J, Holste J, Bunk B, Freese HM, Spröer C, Dlugosch L, Kück AC, Schulz S, Brinkhoff T. High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus. Front Microbiol 2021; 12:688754. [PMID: 34262548 PMCID: PMC8273931 DOI: 10.3389/fmicb.2021.688754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.
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Affiliation(s)
- Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jonas Holste
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Heike M. Freese
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Anna-Carlotta Kück
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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20
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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21
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Um S, Seibel E, Schalk F, Balluff S, Beemelmanns C. Targeted Isolation of Saalfelduracin B-D from Amycolatopsis saalfeldensis Using LC-MS/MS-Based Molecular Networking. JOURNAL OF NATURAL PRODUCTS 2021; 84:1002-1011. [PMID: 33683882 DOI: 10.1021/acs.jnatprod.0c01027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High-resolution tandem mass spectrometry (HR-MS2)-based metabolomic studies of Amycolatopsis saalfeldensis, isolated from the "Saalfelder Feengrotten" caves in Germany, led to the isolation of three ribosomally synthesized and post-translationally modified type II thiopeptides, saalfelduracin B-D (1-3) and the known saalfelduracin A (4). The structures of all four compounds were determined by comparative two-dimensional NMR analysis and high-resolution tandem mass spectrometry.
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Affiliation(s)
- Soohyun Um
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Elena Seibel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Felix Schalk
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Sven Balluff
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
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22
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Mazorra-Alonso M, Tomás G, Soler JJ. Microbially Mediated Chemical Ecology of Animals: A Review of Its Role in Conspecific Communication, Parasitism and Predation. BIOLOGY 2021; 10:274. [PMID: 33801728 PMCID: PMC8065758 DOI: 10.3390/biology10040274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
Microbial symbionts are nowadays considered of pivotal importance for animal life. Among the many processes where microorganisms are involved, an emerging research avenue focuses on their major role in driving the evolution of chemical communication in their hosts. Volatiles of bacterial origin may underlie chemical communication and the transfer of social information through signals, as well as inadvertent social information. We reviewed the role of microorganisms in animal communication between conspecifics, and, because the microbiome may cause beneficial as well as deleterious effects on their animal hosts, we also reviewed its role in determining the outcome of the interactions with parasites and predators. Finally, we paid special attention to the hypothetical role of predation and parasitism in driving the evolution of the animal microbiome. We highlighted the novelty of the theoretical framework derived from considering the microbiota of animals in scenarios of communication, parasitism, and predation. We aimed to encourage research in these areas, suggesting key predictions that need to be tested to better understand what is one of the main roles of bacteria in animal biology.
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Affiliation(s)
- Mónica Mazorra-Alonso
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
| | - Gustavo Tomás
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
- Unidad Asociada (Consejo Superior de Investigaciones Científicas): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071 Granada, Spain
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, 04120 Almería, Spain
- Unidad Asociada (Consejo Superior de Investigaciones Científicas): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071 Granada, Spain
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23
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Mahler L, Niehs SP, Martin K, Weber T, Scherlach K, Hertweck C, Roth M, Rosenbaum MA. Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities. eLife 2021; 10:64774. [PMID: 33764297 PMCID: PMC8081529 DOI: 10.7554/elife.64774] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.
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Affiliation(s)
- Lisa Mahler
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sarah P Niehs
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Karin Martin
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Thomas Weber
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Kirstin Scherlach
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.,Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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Atanasov AG, Zotchev SB, Dirsch VM, Supuran CT. Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov 2021; 20:200-216. [PMID: 33510482 PMCID: PMC7841765 DOI: 10.1038/s41573-020-00114-z] [Citation(s) in RCA: 1770] [Impact Index Per Article: 590.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.
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Affiliation(s)
- Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, Poland.
- Department of Pharmacognosy, University of Vienna, Vienna, Austria.
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Verena M Dirsch
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Florence, Italy.
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Danelius E, Halaby S, van der Donk WA, Gonen T. MicroED in natural product and small molecule research. Nat Prod Rep 2021; 38:423-431. [PMID: 32939523 PMCID: PMC7965795 DOI: 10.1039/d0np00035c] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA 90095, USA.
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Schlembach I, Grünberger A, Rosenbaum MA, Regestein L. Measurement Techniques to Resolve and Control Population Dynamics of Mixed-Culture Processes. Trends Biotechnol 2021; 39:1093-1109. [PMID: 33573846 PMCID: PMC7612867 DOI: 10.1016/j.tibtech.2021.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial mixed cultures are gaining increasing attention as biotechnological production systems, since they offer a large but untapped potential for future bioprocesses. Effects of secondary metabolite induction and advantages of labor division for the degradation of complex substrates offer new possibilities for process intensification. However, mixed cultures are highly complex, and, consequently, many biotic and abiotic parameters are required to be identified, characterized, and ideally controlled to establish a stable bioprocess. In this review, we discuss the advantages and disadvantages of existing measurement techniques for identifying, characterizing, monitoring, and controlling mixed cultures and highlight promising examples. Moreover, existing challenges and emerging technologies are discussed, which lay the foundation for novel analytical workflows to monitor mixed-culture bioprocesses.
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Affiliation(s)
- Ivan Schlembach
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany; Faculty for Biological Sciences, Friedrich-Schiller-University Jena, Bachstrasse 18K, 07743 Jena, Germany
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Adolf-Reichwein-Str. 23, 07745 Jena, Germany.
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27
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Maher AMD, Asaiyah M, Quinn S, Burke R, Wolff H, Bode HB, Griffin CT. Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host. MICROBIAL ECOLOGY 2021; 81:223-239. [PMID: 32827089 DOI: 10.1007/s00248-020-01573-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.
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Affiliation(s)
- Abigail M D Maher
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Mohamed Asaiyah
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Sarajane Quinn
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Riona Burke
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - Hendrik Wolff
- Molecular Biotechnology, Department of Biosciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, and Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, and Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany
| | - Christine T Griffin
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland.
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Lee SR, Guo H, Yu JS, Park M, Dahse HM, Jung WH, Beemelmanns C, Kim KH. Revised structural assignment of azalomycins based on genomic and chemical analysis. Org Chem Front 2021. [DOI: 10.1039/d1qo00610j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We clarified structural inconsistencies of four azalomycin derivatives (F4a, F4b, F5a and F5b) from Streptomyces sp. M56 by nuclear magnetic resonance, J-based configuration analyses, electronic circular dichroism and in silico genome studies.
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Affiliation(s)
- Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry, Princeton University, New Jersey 08544, USA
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jae Sik Yu
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Minji Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Maglangit F, Yu Y, Deng H. Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens). Nat Prod Rep 2021; 38:782-821. [PMID: 33119013 DOI: 10.1039/d0np00061b] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to the second quarter of 2020 Threat or treat? While pathogenic bacteria pose significant threats, they also represent a huge reservoir of potential pharmaceuticals to treat various diseases. The alarming antimicrobial resistance crisis and the dwindling clinical pipeline urgently call for the discovery and development of new antibiotics. Pathogenic bacteria have an enormous potential for natural products drug discovery, yet they remained untapped and understudied. Herein, we review the specialised metabolites isolated from entomopathogenic, phytopathogenic, and human pathogenic bacteria with antibacterial and antifungal activities, highlighting those currently in pre-clinical trials or with potential for drug development. Selected unusual biosynthetic pathways, the key roles they play (where known) in various ecological niches are described. We also provide an overview of the mode of action (molecular target), activity, and minimum inhibitory concentration (MIC) towards bacteria and fungi. The exploitation of pathogenic bacteria as a rich source of antimicrobials, combined with the recent advances in genomics and natural products research methodology, could pave the way for a new golden age of antibiotic discovery. This review should serve as a compendium to communities of medicinal chemists, organic chemists, natural product chemists, biochemists, clinical researchers, and many others interested in the subject.
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Affiliation(s)
- Fleurdeliz Maglangit
- Department of Biology and Environmental Science, College of Science, University of the Philippines Cebu, Lahug, Cebu City, 6000, Philippines. and Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, UK.
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30
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Rak Lee S, Schalk F, Schwitalla JW, Benndorf R, Vollmers J, Kaster AK, de Beer ZW, Park M, Ahn MJ, Jung WH, Beemelmanns C, Kim KH. Polyhalogenation of Isoflavonoids by the Termite-Associated Actinomadura sp. RB99. JOURNAL OF NATURAL PRODUCTS 2020; 83:3102-3110. [PMID: 32946237 DOI: 10.1021/acs.jnatprod.0c00676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Based on high-resolution tandem mass spectrometry (HR-MS2) and global natural products social molecular networking (GNPS), we found that plant-derived daidzein and genistein derivatives are polyhalogenated by termite-associated Actinomadura species RB99. MS-guided purification from extracts of bacteria grown under optimized conditions led to the isolation of eight polychlorinated isoflavones, including six unreported derivatives, and seven novel polybrominated derivatives, two of which showed antimicrobial activity.
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Affiliation(s)
- Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Felix Schalk
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Jan W Schwitalla
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, Pretoria, South Africa
| | - Minji Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Mi-Jeong Ahn
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Won Hee Jung
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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31
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Abstract
Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated bacterial-fungal interrelations. We discuss pairwise interactions among defined species and systems involving additional organisms as well as complex interactions among microbial communities encountered in the soil or defined as microbiota of higher organisms. Finally, we give examples of how the growing understanding of microbial interactions has contributed to drug discovery and hypothesize what may be future directions in studying and engineering microbiota for agricultural or medicinal purposes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07745 Jena, Germany
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32
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In Situ Activation and Heterologous Production of a Cryptic Lantibiotic from an African Plant Ant-Derived Saccharopolyspora Species. Appl Environ Microbiol 2020; 86:AEM.01876-19. [PMID: 31732571 PMCID: PMC6974636 DOI: 10.1128/aem.01876-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/07/2019] [Indexed: 01/05/2023] Open
Abstract
The discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here, we report a strategy for the ectopic expression of pathway-specific positive regulators that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression. Most clinical antibiotics are derived from actinomycete natural products discovered at least 60 years ago. However, the repeated rediscovery of known compounds led the pharmaceutical industry to largely discard microbial natural products (NPs) as a source of new chemical diversity. Recent advances in genome sequencing have revealed that these organisms have the potential to make many more NPs than previously thought. Approaches to unlock NP biosynthesis by genetic manipulation of strains, by the application of chemical genetics, or by microbial cocultivation have resulted in the identification of new antibacterial compounds. Concomitantly, intensive exploration of coevolved ecological niches, such as insect-microbe defensive symbioses, has revealed these to be a rich source of chemical novelty. Here, we report the new lanthipeptide antibiotic kyamicin, which was generated through the activation of a cryptic biosynthetic gene cluster identified by genome mining Saccharopolyspora species found in the obligate domatium-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. Transcriptional activation of this silent gene cluster was achieved by ectopic expression of a pathway-specific activator under the control of a constitutive promoter. Subsequently, a heterologous production platform was developed which enabled the purification of kyamicin for structural characterization and bioactivity determination. This strategy was also successful for the production of lantibiotics from other genera, paving the way for a synthetic heterologous expression platform for the discovery of lanthipeptides that are not detected under laboratory conditions or that are new to nature. IMPORTANCE The discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here, we report a strategy for the ectopic expression of pathway-specific positive regulators that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression.
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33
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Liu C, Kakeya H. Cryptic Chemical Communication: Secondary Metabolic Responses Revealed by Microbial Co‐culture. Chem Asian J 2020; 15:327-337. [DOI: 10.1002/asia.201901505] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/15/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Chao Liu
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University Sakyo-ku Kyoto 606-8501 Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular SciencesDivision of Bioinformatics and Chemical GenomicsGraduate School of Pharmaceutical SciencesKyoto University Sakyo-ku Kyoto 606-8501 Japan
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Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem 2020; 295:34-54. [PMID: 31784450 PMCID: PMC6952617 DOI: 10.1074/jbc.rev119.006545] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
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Bode E, Heinrich AK, Hirschmann M, Abebew D, Shi Y, Vo TD, Wesche F, Shi Y, Grün P, Simonyi S, Keller N, Engel Y, Wenski S, Bennet R, Beyer S, Bischoff I, Buaya A, Brandt S, Cakmak I, Çimen H, Eckstein S, Frank D, Fürst R, Gand M, Geisslinger G, Hazir S, Henke M, Heermann R, Lecaudey V, Schäfer W, Schiffmann S, Schüffler A, Schwenk R, Skaljac M, Thines E, Thines M, Ulshöfer T, Vilcinskas A, Wichelhaus TA, Bode HB. Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing. Angew Chem Int Ed Engl 2019; 58:18957-18963. [PMID: 31693786 PMCID: PMC6972681 DOI: 10.1002/anie.201910563] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Indexed: 12/02/2022]
Abstract
Natural products (NPs) from microorganisms have been important sources for discovering new therapeutic and chemical entities. While their corresponding biosynthetic gene clusters (BGCs) can be easily identified by gene-sequence-similarity-based bioinformatics strategies, the actual access to these NPs for structure elucidation and bioactivity testing remains difficult. Deletion of the gene encoding the RNA chaperone, Hfq, results in strains losing the production of most NPs. By exchanging the native promoter of a desired BGC against an inducible promoter in Δhfq mutants, almost exclusive production of the corresponding NP from the targeted BGC in Photorhabdus, Xenorhabdus and Pseudomonas was observed including the production of several new NPs derived from previously uncharacterized non-ribosomal peptide synthetases (NRPS). This easyPACId approach (easy Promoter Activated Compound Identification) facilitates NP identification due to low interference from other NPs. Moreover, it allows direct bioactivity testing of supernatants containing secreted NPs, without laborious purification.
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36
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Bode E, Heinrich AK, Hirschmann M, Abebew D, Shi Y, Vo TD, Wesche F, Shi Y, Grün P, Simonyi S, Keller N, Engel Y, Wenski S, Bennet R, Beyer S, Bischoff I, Buaya A, Brandt S, Cakmak I, Çimen H, Eckstein S, Frank D, Fürst R, Gand M, Geisslinger G, Hazir S, Henke M, Heermann R, Lecaudey V, Schäfer W, Schiffmann S, Schüffler A, Schwenk R, Skaljac M, Thines E, Thines M, Ulshöfer T, Vilcinskas A, Wichelhaus TA, Bode HB. Promoter Activation in Δ
hfq
Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Velasco-Alzate KY, Bauermeister A, Tangerina MMP, Lotufo TMC, Ferreira MJP, Jimenez PC, Padilla G, Lopes NP, Costa-Lotufo LV. Marine Bacteria from Rocas Atoll as a Rich Source of Pharmacologically Active Compounds. Mar Drugs 2019; 17:md17120671. [PMID: 31795148 PMCID: PMC6949966 DOI: 10.3390/md17120671] [Citation(s) in RCA: 8] [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: 10/17/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 12/24/2022] Open
Abstract
Rocas Atoll is a unique environment in the equatorial Atlantic Ocean, hosting a large number of endemic species, however, studies on the chemical diversity emerging from this biota are rather scarce. Therefore, the present work aims to assess the metabolomic diversity and pharmacological potential of the microbiota from Rocas Atoll. A total of 76 bacteria were isolated and cultured in liquid culture media to obtain crude extracts. About one third (34%) of these extracts were recognized as cytotoxic against human colon adenocarcinoma HCT-116 cell line. 16S rRNA gene sequencing analyses revealed that the bacteria producing cytotoxic extracts were mainly from the Actinobacteria phylum, including Streptomyces, Salinispora, Nocardiopsis, and Brevibacterium genera, and in a smaller proportion from Firmicutes phylum (Bacillus). The search in the spectral library in GNPS (Global Natural Products Social Molecular Networking) unveiled a high chemodiversity being produced by these bacteria, including rifamycins, antimycins, desferrioxamines, ferrioxamines, surfactins, surugamides, staurosporines, and saliniketals, along with several unidentified compounds. Using an original approach, molecular networking successfully highlighted groups of compounds responsible for the cytotoxicity of crude extracts. Application of DEREPLICATOR+ (GNPS) allowed the annotation of macrolide novonestimycin derivatives as the cytotoxic compounds existing in the extracts produced by Streptomyces BRB-298 and BRB-302. Overall, these results highlighted the pharmacological potential of bacteria from this singular atoll.
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Affiliation(s)
- Karen Y. Velasco-Alzate
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
| | - Anelize Bauermeister
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
- NPPNS, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto/SP, Brazil;
| | - Marcelo M. P. Tangerina
- Departamento do Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo/SP, Brazil (M.J.P.F.)
| | - Tito M. C. Lotufo
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, 05508-120 São Paulo/SP, Brazil;
| | - Marcelo J. P. Ferreira
- Departamento do Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo/SP, Brazil (M.J.P.F.)
| | - Paula C. Jimenez
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, 11015-020 Santos/SP, Brazil;
| | - Gabriel Padilla
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil;
| | - Norberto P. Lopes
- NPPNS, Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto/SP, Brazil;
| | - Letícia V. Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, 05508-900 São Paulo/SP, Brazil; (K.Y.V.-A.); (A.B.)
- Correspondence: or ; Tel.: +55-11-30917316
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38
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Zhang C, Straight PD. Antibiotic discovery through microbial interactions. Curr Opin Microbiol 2019; 51:64-71. [DOI: 10.1016/j.mib.2019.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/20/2019] [Indexed: 01/09/2023]
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Frioux C, Fremy E, Trottier C, Siegel A. Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. Bioinformatics 2019; 34:i934-i943. [PMID: 30423063 PMCID: PMC6129287 DOI: 10.1093/bioinformatics/bty588] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Motivation The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far. Results We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria. Availability and implementation Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.
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Affiliation(s)
| | - Enora Fremy
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
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40
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Diettrich J, Kage H, Nett M. Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1. Beilstein J Org Chem 2019; 15:1298-1303. [PMID: 31293678 PMCID: PMC6604713 DOI: 10.3762/bjoc.15.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
A putative siderophore locus was detected in the genome of the violacein-producing bacterium Massilia sp. NR 4-1 and predicted to direct the biosynthesis of a molecule that is structurally related to the thiazoline-containing siderophore micacocidin. In order to track this compound, we analyzed the metabolic profiles of Massilia cultures grown under different iron concentrations. A compound which was found to be predominantly produced under iron deficiency was subsequently isolated. Its structural characterization by spectroscopic and bioinformatic analyses revealed a previously not known diastereomer of the cytotoxic alkaloid agrochelin. The structure of this natural product, which was named massiliachelin, corresponds to the assembly line encoded by the identified siderophore locus.
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Affiliation(s)
- Jan Diettrich
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Hirokazu Kage
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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41
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Dose B, Niehs SP, Scherlach K, Flórez LV, Kaltenpoth M, Hertweck C. Unexpected Bacterial Origin of the Antibiotic Icosalide: Two-Tailed Depsipeptide Assembly in Multifarious Burkholderia Symbionts. ACS Chem Biol 2018; 13:2414-2420. [PMID: 30160099 DOI: 10.1021/acschembio.8b00600] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Icosalide is an unusual two-tailed lipocyclopeptide antibiotic that was originally isolated from a fungal culture. Yet, its biosynthesis and ecological function have remained enigmatic. By genome mining and metabolic profiling of a bacterial endosymbiont ( Burkholderia gladioli) of the pest beetle Lagria villosa, we unveiled a bacterial origin of icosalide. Functional analysis of the biosynthetic gene locus revealed an unprecedented nonribosomal peptide synthetase (NRPS) that incorporates two β-hydroxy acids by means of two starter condensation domains in different modules. This unusual assembly line, which may inspire new synthetic biology approaches, is widespread among many symbiotic Burkholderia species from diverse habitats. Biological assays showed that icosalide is active against entomopathogenic bacteria, thus adding to the chemical armory protecting beetle offspring. By creating a null mutant, we found that icosalide is a swarming inhibitor, which may play a role in symbiotic interactions and bears the potential for therapeutic applications.
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Affiliation(s)
- Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Laura V. Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128 Mainz, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
- Friedrich Schiller University Jena, 07743 Jena, Germany
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42
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Benndorf R, Guo H, Sommerwerk E, Weigel C, Garcia-Altares M, Martin K, Hu H, Küfner M, de Beer ZW, Poulsen M, Beemelmanns C. Natural Products from Actinobacteria Associated with Fungus-Growing Termites. Antibiotics (Basel) 2018; 7:E83. [PMID: 30217010 PMCID: PMC6165096 DOI: 10.3390/antibiotics7030083] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 12/03/2022] Open
Abstract
The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.
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Affiliation(s)
- René Benndorf
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Elisabeth Sommerwerk
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Maria Garcia-Altares
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Karin Martin
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Haofu Hu
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Michelle Küfner
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
| | - Z Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agriculture Biotechnology Institute, University of Pretoria, Pretoria 0001, South Africa.
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark.
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.
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43
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Role of Chemical Mediators in Aquatic Interactions across the Prokaryote-Eukaryote Boundary. J Chem Ecol 2018; 44:1008-1021. [PMID: 30105643 DOI: 10.1007/s10886-018-1004-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/24/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
There is worldwide growing interest in the occurrence and diversity of metabolites used as chemical mediators in cross-kingdom interactions within aquatic systems. Bacteria produce metabolites to protect and influence the growth and life cycle of their eukaryotic hosts. In turn, the host provides a nutrient-enriched environment for the bacteria. Here, we discuss the role of waterborne chemical mediators that are responsible for such interactions in aquatic multi-partner systems, including algae or invertebrates and their associated bacteria. In particular, this review highlights recent advances in the chemical ecology of aquatic systems that support the overall ecological significance of signaling molecules across the prokaryote-eukaryote boundary (cross-kingdom interactions) for growth, development and morphogenesis of the host. We emphasize the value of establishing well-characterized model systems that provide the basis for the development of ecological principles that represent the natural lifestyle and dynamics of aquatic microbial communities and enable a better understanding of the consequences of environmental change and the most effective means of managing community interactions.
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44
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Guo H, Benndorf R, König S, Leichnitz D, Weigel C, Peschel G, Berthel P, Kaiser M, Steinbeck C, Werz O, Poulsen M, Beemelmanns C. Expanding the Rubterolone Family: Intrinsic Reactivity and Directed Diversification of PKS-derived Pyrans. Chemistry 2018; 24:11319-11324. [PMID: 29846024 DOI: 10.1002/chem.201802066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/26/2018] [Indexed: 12/20/2022]
Abstract
We characterized two key biosynthetic intermediates of the intriguing rubterolone family (tropolone alkaloids) that contain a highly reactive pyran moiety (in equilibrium with the hydrolyzed 1,5-dione form) and undergo spontaneous pyridine formation in the presence of primary amines. We exploited the intrinsic reactivity of the pyran moiety and isolated several new rubterolone derivatives, two of which contain a unique thiazolidine moiety. Three rubterolone derivatives were chemically modified with fluorescence and biotin tags using peptide coupling and click reaction. Overall, eight derivatives were fully characterized by HRMS/MS and 1D and 2D NMR spectroscopy and their antimicrobial, cytotoxic, anti-inflammatory and antiparasitic activities evaluated.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - René Benndorf
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Stefanie König
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Daniel Leichnitz
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Gundela Peschel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Patrick Berthel
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Parasite Chemotherapy, Socinstraße 57, 4002, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Christoph Steinbeck
- Institute for Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743, Jena, Germany
| | - Michael Poulsen
- Centre for Social Evolution, University of Copenhagen, 2100, Copenhagen East, Denmark
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research, and Infection Biology-Hans Knöll Institute, Beutenbergstraße 11a, 07745, Jena, Germany
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45
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Flórez LV, Scherlach K, Miller IJ, Rodrigues A, Kwan JC, Hertweck C, Kaltenpoth M. An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles. Nat Commun 2018; 9:2478. [PMID: 29946103 PMCID: PMC6018673 DOI: 10.1038/s41467-018-04955-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Microbial symbionts are often a source of chemical novelty and can contribute to host defense against antagonists. However, the ecological relevance of chemical mediators remains unclear for most systems. Lagria beetles live in symbiosis with multiple strains of Burkholderia bacteria that protect their offspring against pathogens. Here, we describe the antifungal polyketide lagriamide, and provide evidence supporting that it is produced by an uncultured symbiont, Burkholderia gladioli Lv-StB, which is dominant in field-collected Lagria villosa. Interestingly, lagriamide is structurally similar to bistramides, defensive compounds found in marine tunicates. We identify a gene cluster that is probably involved in lagriamide biosynthesis, provide evidence for horizontal acquisition of these genes, and show that the naturally occurring symbiont strains on the egg are protective in the soil environment. Our findings highlight the potential of microbial symbionts and horizontal gene transfer as influential sources of ecological innovation.
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Affiliation(s)
- Laura V Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany.
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Ian J Miller
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP-São Paulo State University, Av. 24A, n. 1515-Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Jason C Kwan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
- Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany
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46
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Netzker T, Flak M, Krespach MK, Stroe MC, Weber J, Schroeckh V, Brakhage AA. Microbial interactions trigger the production of antibiotics. Curr Opin Microbiol 2018; 45:117-123. [PMID: 29702423 DOI: 10.1016/j.mib.2018.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 11/30/2022]
Abstract
Since the discovery of penicillin, antibiotics have been instrumental in treating infectious diseases. However, emerging antibiotic multi-resistance coinciding with a nearly exhausted drug pipeline is a major concern for the future of the therapy of infections. A novel approach for the discovery of antibiotics relies on the analysis of microbial consortia in their ecological context, taking into account the potential natural role of antibiotics. Co-cultivations of microorganisms have been successfully applied for the isolation of unknown secondary metabolites including antibiotics, and, thus, open new avenues to the production of bioactive compounds while at the same time providing insight into the natural function of the produced molecules and the regulation of their formation.
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Affiliation(s)
- Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Michal Flak
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Mario Kc Krespach
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Maria C Stroe
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany; Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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