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Zhou Z, Yang J, Ma J, Shang Z, Fang R, Tian X, Li Q, Ju J. Antarmycins: Discovery, Biosynthesis, Anti-pathogenic Bacterial Activity, and Mechanism of Action from Deep-Sea-Derived Pseudonocardia antarctica. JACS AU 2025; 5:237-249. [PMID: 39886587 PMCID: PMC11775689 DOI: 10.1021/jacsau.4c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 12/07/2024] [Accepted: 12/09/2024] [Indexed: 02/01/2025]
Abstract
The rapid emergence of antimicrobial-resistant pathogenic microbes has accelerated the search for novel therapeutic agents. Here we report the discovery of antarmycin A (1), an antibiotic containing a symmetric 16-membered macrodiolide core with two pendant vancosamine moieties, one of which is glucosylated, from deep-sea-derived Pseudonocardia antarctica SCSIO 07407. The biosynthetic gene cluster of 1 was identified on a giant plasmid featuring transferable elements. In-depth biosynthetic investigation enabled us to (i) identify a set of seven genes associated with the product of the vancosamine moiety; (ii) discover two glycosyltransferases dedicated to the transfer of pendant sugars; and (iii) isolate rhamnose-modified antarmycin B (2) and a deglucosylated derivative antarmycin C (3) from genetically engineered mutant strains. Antibacterial assays revealed that 1 displays superior antibacterial properties with potent in vitro activities against the critical priority pathogens, multidrug-resistant Enterococcus faecium and methicillin-resistant Staphylococcus aureus, fast bacterial killing, insusceptibility to antimicrobial resistance, and high in vivo efficiency in infection models. Mechanistic investigations revealed that 1 disrupts the bacterial cell membrane through a mechanism involving interactions between the vancosamine moieties and membrane-embedded phosphatidylglycerol/phosphatidylethanolamine. The results provide insights into the biological generation of vancosamine in natural products and demonstrate the potential of 1 as an effective lead to address the growing antimicrobial resistance threats.
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Affiliation(s)
- Zhenbin Zhou
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, Qingdao 266400, China
| | - Jiafan Yang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, Qingdao 266400, China
| | - Junying Ma
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Zhuo Shang
- Key
Laboratory of Chemical Biology (Ministry of Education), Shandong Basic
Science Research Center (Pharmacy), School of Pharmaceutical Sciences,
Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Runping Fang
- Key
Laboratory of Chemical Biology (Ministry of Education), Shandong Basic
Science Research Center (Pharmacy), School of Pharmaceutical Sciences,
Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Xinpeng Tian
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Qinglian Li
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jianhua Ju
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Key
Laboratory of Chemical Biology (Ministry of Education), Shandong Basic
Science Research Center (Pharmacy), School of Pharmaceutical Sciences,
Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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2
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Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
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Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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3
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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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4
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Diarra U, Osborne-Naikatini T. Isolation, characterization and screening of actinomycetes associated with fijian ant-plant symbioses. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37938888 DOI: 10.1099/mic.0.001410] [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: 11/10/2023]
Abstract
In the search for novel therapeutics to combat the ongoing antimicrobial resistance crisis, scientists are turning to underexplored environments. Defensive mutualisms between hymenopteran insects and actinomycetes represent important reservoirs for bioactive compounds. In this study, we examined the association between actinomycetes and Squamellaria ant-plants spanning three different ant and plant species combinations (Squamellaria imberbis-Philidris nagasau, Squamellaria tenuiflora- Technomyrmex vitiensis, and Squamellaria tenuiflora-Tetramorium insolens). Eight Squamellaria plants were sampled including four containing T. vitiensis, three containing P. nagasau, and a single plant containing T. insolens. A total of 47 actinomycetes were obtained from the sampled material, with 5, 16, and 26 isolates originating from cuticle, tissue, and nest samples, respectively. Cross-streaking tests showed that 12 out of 47 isolates inhibited bacterial pathogens. The most frequently inhibited pathogens in the cross-streaking tests were S. aureus and E. coli while S. enterica was the least inhibited. Among the three primary screening media used, ISP2 agar was the most suitable for secondary metabolism as more isolates exhibited antibacterial activity when grown on the medium. TFS2010 and TFS2003, which matched to Streptomyces gramineus (>99% similarity), were the most bioactive isolates in cross-streaking tests. TFS2010 displayed the strong antibacterial on Nutrient agar, Mueller Hinton agar, and ISP2 agar while TFS2003 only exhibited strong antibacterial activity on Nutrient agar. Furthermore, a difference in potency of extracts based on batch culture medium was noted in TFS2010. DNA was extracted from 19 isolates and followed by 16SrRNA gene sequencing. Analysis of sequence data revealed the presence of six genera, including Amycolatopsis, Asanoa, Jiangella, Nocardia, Nocardiopsis, and Streptomyces, with the latter being the most abundant taxon. Among these, three isolates (PNS3002, PNS3005, and TFS3001) are likely to represent new species while one (TFS2015) is likely to be a member of a novel genus. Our work represents the first attempt to study actinomycetes from Squamellaria-ant mutualisms.
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Affiliation(s)
- Umar Diarra
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences, The University of the South Pacific, Laucala Campus, Suva, Fiji
| | - Tamara Osborne-Naikatini
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences, The University of the South Pacific, Laucala Campus, Suva, Fiji
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Yakkala PA, Penumallu NR, Shafi S, Kamal A. Prospects of Topoisomerase Inhibitors as Promising Anti-Cancer Agents. Pharmaceuticals (Basel) 2023; 16:1456. [PMID: 37895927 PMCID: PMC10609717 DOI: 10.3390/ph16101456] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Topoisomerases are very important enzymes that regulate DNA topology and are vital for biological actions like DNA replication, transcription, and repair. The emergence and spread of cancer has been intimately associated with topoisomerase dysregulation. Topoisomerase inhibitors have consequently become potential anti-cancer medications because of their ability to obstruct the normal function of these enzymes, which leads to DNA damage and subsequently causes cell death. This review emphasizes the importance of topoisomerase inhibitors as marketed, clinical and preclinical anti-cancer medications. In the present review, various types of topoisomerase inhibitors and their mechanisms of action have been discussed. Topoisomerase I inhibitors, which include irinotecan and topotecan, are agents that interact with the DNA-topoisomerase I complex and avert resealing of the DNA. The accretion of DNA breaks leads to the inhibition of DNA replication and cell death. On the other hand, topoisomerase II inhibitors like etoposide and teniposide, function by cleaving the DNA-topoisomerase II complex thereby effectively impeding the release of double-strand DNA breaks. Moreover, the recent advances in exploring the therapeutic efficacy, toxicity, and MDR (multidrug resistance) issues of new topoisomerase inhibitors have been reviewed in the present review.
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Affiliation(s)
- Prasanna Anjaneyulu Yakkala
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India;
| | - Naveen Reddy Penumallu
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India;
| | - Syed Shafi
- Department of Chemistry, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India;
| | - Ahmed Kamal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India;
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Hyderabad Campus, Dist. Medchal, Hyderabad 500078, India
- Telangana State Council of Science & Technology, Environment, Forests, Science & Technology Department, Hyderabad 500004, India
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6
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Amycolatopsis from Desert Specialist Fungus-Growing Ants Suppresses Contaminant Fungi Using the Antibiotic ECO-0501. Appl Environ Microbiol 2023; 89:e0183822. [PMID: 36700628 PMCID: PMC9972958 DOI: 10.1128/aem.01838-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Symbiotic Actinobacteria help fungus-growing ants suppress fungal pathogens through the production of antifungal compounds. Trachymyrmex ants of the southwest desert of the United States inhabit a unique niche far from the tropical rainforests in which most fungus-growing ant species are found. These ants may not encounter the specialist fungal pathogen Escovopsis known to threaten colonies of other fungus-growing ants. It is unknown whether Actinobacteria associated with these ants antagonize contaminant fungi and, if so, what the chemical basis of such antagonism is. We find that Pseudonocardia and Amycolatopsis strains isolated from three desert specialist Trachymyrmex species do antagonize diverse contaminant fungi isolated from field-collected ant colonies. We did not isolate the specialist fungal pathogen Escovopsis in our sampling. We trace strong antifungal activity from Amycolatopsis isolates to the molecule ECO-0501, an antibiotic that was previously under preclinical development as an antibacterial agent. In addition to suppression of contaminant fungi, we find that this molecule has strong activity against ant-associated Actinobacteria and may also play a role in bacterial competition in this niche. By studying interspecies interactions in a previously unexplored niche, we have uncovered novel bioactivity for a structurally unique antibiotic. IMPORTANCE Animal hosts often benefit from chemical defenses provided by microbes. These molecular defenses are a potential source of novel antibiotics and offer opportunities for understanding how antibiotics are used in ecological contexts with defined interspecies interactions. Here, we recover contaminant fungi from nests of Trachymyrmex fungus-growing ants of the southwest desert of the United States and find that they are suppressed by Actinobacteria isolated from these ants. The antibiotic ECO-0501 is an antifungal agent used by some of these Amycolatopsis bacterial isolates. This antibiotic was previously investigated in preclinical studies and known only for antibacterial activity.
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7
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Hansen KA, Kim RR, Lawton ES, Tran J, Lewis SK, Deol AS, Van Arnam EB. Bacterial Associates of a Desert Specialist Fungus-Growing Ant Antagonize Competitors with a Nocamycin Analog. ACS Chem Biol 2022; 17:1824-1830. [PMID: 35730734 DOI: 10.1021/acschembio.2c00187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fungus-growing ants are defended by antibiotic-producing bacterial symbionts in the genus Pseudonocardia. Nutrients provisioned by the ants support these symbionts but also invite colonization and competition from other bacteria. As an arena for chemically mediated bacterial competition, this niche offers a window into ecological antibiotic function with well-defined competing organisms. From multiple colonies of the desert specialist ant Trachymyrmex smithi, we isolated Amycolatopsis bacteria that inhibit the growth of Pseudonocardia symbionts under laboratory conditions. Using bioassay-guided fractionation, we discovered a novel analog of the antibiotic nocamycin that is responsible for this antagonism. We identified the biosynthetic gene cluster for this antibiotic, which has a suite of oxidative enzymes consistent with this molecule's more extensive oxidative tailoring relative to similar tetramic acid antibiotics. High genetic similarity to globally distributed soil Amycolatopsis isolates suggest that this ant-derived Amycolatopsis strain may be an opportunistic soil strain whose antibiotic production allows for competition in this specialized niche. This nocamycin analog adds to the catalog of novel bioactive molecules isolated from bacterial associates of fungus-growing ants, and its activity against ant symbionts represents, to our knowledge, the first putative ecological function for the widely distributed enoyl tetramic acid family of antibiotics.
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Affiliation(s)
- Katherine A Hansen
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Rose R Kim
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Elisabeth S Lawton
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Janet Tran
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Stephanie K Lewis
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Arjan S Deol
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Ethan B Van Arnam
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
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8
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Hemmerling F, Piel J. Strategies to access biosynthetic novelty in bacterial genomes for drug discovery. Nat Rev Drug Discov 2022; 21:359-378. [PMID: 35296832 DOI: 10.1038/s41573-022-00414-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.
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Affiliation(s)
- Franziska Hemmerling
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
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9
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Paik A, Paul S, Bhowmik S, Das R, Naveen T, Rana S. Recent Advances in First Row Transition Metal Mediated C‐H Halogenation of (Hetero)arenes and Alkanes. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aniruddha Paik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabarni Paul
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Sabyasachi Bhowmik
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Rahul Das
- University of North Bengal Department of Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India - 734013 734013 Siliguri INDIA
| | - Togati Naveen
- Sardar Vallabhbhai National Institute of Technology Department of Chemistry 395007 Surat INDIA
| | - Sujoy Rana
- University of North Bengal Chemistry Raja Rammohunpur, DarjeelingWest Bengal, India, 734013 734013 Siliguri INDIA
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Caffrey P, Hogan M, Song Y. New Glycosylated Polyene Macrolides: Refining the Ore from Genome Mining. Antibiotics (Basel) 2022; 11:334. [PMID: 35326797 PMCID: PMC8944477 DOI: 10.3390/antibiotics11030334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 01/26/2023] Open
Abstract
Glycosylated polyene macrolides include effective antifungal agents, such as pimaricin, nystatin, candicidin, and amphotericin B. For the treatment of systemic mycoses, amphotericin B has been described as a gold-standard antibiotic because of its potent activity against a broad spectrum of fungal pathogens, which do not readily become resistant. However, amphotericin B has severe toxic side effects, and the development of safer alternatives remains an important objective. One approach towards obtaining such compounds is to discover new related natural products. Advances in next-generation sequencing have delivered a wealth of microbial genome sequences containing polyene biosynthetic gene clusters. These typically encode a modular polyketide synthase that catalyzes the assembly of the aglycone core, a cytochrome P450 that oxidizes a methyl branch to a carboxyl group, and additional enzymes for synthesis and attachment of a single mycosamine sugar residue. In some cases, further P450s catalyze epoxide formation or hydroxylation within the macrolactone. Bioinformatic analyses have identified over 250 of these clusters. Some are predicted to encode potentially valuable new polyenes that have not been uncovered by traditional screening methods. Recent experimental studies have characterized polyenes with new polyketide backbones, previously unknown late oxygenations, and additional sugar residues that increase water-solubility and reduce hemolytic activity. Here we review these studies and assess how this new knowledge can help to prioritize silent polyene clusters for further investigation. This approach should improve the chances of discovering better antifungal antibiotics.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, D04 V1W8 Dublin, Ireland; (M.H.); (Y.S.)
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11
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Li J, Sang M, Jiang Y, Wei J, Shen Y, Huang Q, Li Y, Ni J. Polyene-Producing Streptomyces spp. From the Fungus-Growing Termite Macrotermes barneyi Exhibit High Inhibitory Activity Against the Antagonistic Fungus Xylaria. Front Microbiol 2021; 12:649962. [PMID: 33868208 PMCID: PMC8047067 DOI: 10.3389/fmicb.2021.649962] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/08/2021] [Indexed: 11/19/2022] Open
Abstract
Fungus-growing termites are engaged in a tripartite mutualism with intestinal microbes and a monocultivar (Termitomyces sp.) in the fungus garden. The termites are often plagued by entomopathogen (Metarhizium anisopliae) and fungus garden is always threatened by competitors (Xylaria spp.). Here, we aim to understand the defensive role of intestinal microbes, the actinomycetes which were isolated from the gut of Macrotermes barneyi. We obtained 44 antifungal isolates, which showed moderate to strong inhibition to Xylaria sp. HPLC analysis indicated that different types of polyenes (tetraene, pentene, and heptaene) existed in the metabolites of 10 strong antifungal Streptomyces strains. Two pentene macrolides (pentamycin and 1′14-dihydroxyisochainin) were firstly purified from Streptomyces strain HF10, both exhibiting higher activity against Xylaria sp. and M. anisopliae than cultivar Termitomyces. Subsequently, tetraene and heptaene related gene disruption assay showed that the mutant strains lost the ability to produce corresponding polyenes, and they also had significantly decreased activities against Xylaria sp. and M. anisopliae compared to that of wild type strains. These results indicate that polyene-producing Streptomyces from the guts of M. barneyi have strong inhibition to competitor fungus and polyenes contribute to inhibitory effects on Xylaria sp.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Moli Sang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yutong Jiang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Jianhua Wei
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Qihong Huang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaoyao Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.,School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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12
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Fukuda TH, Helfrich EJN, Mevers E, Melo WGP, Van Arnam EB, Andes DR, Currie CR, Pupo MT, Clardy J. Specialized Metabolites Reveal Evolutionary History and Geographic Dispersion of a Multilateral Symbiosis. ACS CENTRAL SCIENCE 2021; 7:292-299. [PMID: 33655067 PMCID: PMC7908033 DOI: 10.1021/acscentsci.0c00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 05/29/2023]
Abstract
Fungus-growing ants engage in a multilateral symbiosis: they cultivate a fungal garden as their primary food source and host symbiotic actinobacteria (Pseudonocardia spp.) that provide chemical defenses. The bacterial symbionts produce small specialized metabolites that protect the fungal garden from specific fungal pathogens (Escovopsis spp.), and in return, they are fed by the ant hosts. Multiple studies on the molecules underlying this symbiotic system have led to the discovery of a large number of structurally diverse antifungal molecules, but somewhat surprisingly no shared structural theme emerged from these studies. A large systematic study of Brazilian nests led to the discovery of the widespread production of a potent but overlooked antifungal agent, which we named attinimicin, by nearly two-thirds of all Pseudonocardia strains from multiple sites in Brazil. Here we report the structure of attinimicin, its putative biosynthetic gene cluster, and the evolutionary relationship between attinimicin and two related peptides, oxachelin A and cahuitamycin A. All three nonribosomal peptides are structural isomers with different primary peptide sequences. Attinimicin shows iron-dependent antifungal activity against specific environmental fungal parasites but no activity against the fungal cultivar. Attinimicin showed potent in vivo activity in a mouse Candida albicans infection model comparable to clinically used azole-containing antifungals. In situ detection of attinimicin in both ant nests and on worker ants supports an ecological role for attinimicin in protecting the fungal cultivar from pathogens. The geographic spread of the attinimicin biosynthetic gene cluster in Brazilian Pseudonocardia spp. marks attinimicin as the first specialized metabolite from ant-associated bacteria with broad geographic distribution.
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Affiliation(s)
- Taise
T. H. Fukuda
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- School
of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Eric J. N. Helfrich
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Institute
for Molecular Bio Science, Goethe University
Frankfurt, 60438 Frankfurt am Main, Germany
- LOEWE
Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt
am Main, Germany
| | - Emily Mevers
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Weilan G. P. Melo
- School
of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Ethan B. Van Arnam
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Keck
Science
Department, Claremont McKenna, Pitzer, and
Scripps Colleges, Claremont, California 91711, United States
| | - David R. Andes
- Department
of Medicine, University of Wisconsin School
of Medicine and Public Health, Madison, Wisconsin 53705, United States
| | - Cameron R. Currie
- Department
of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Monica T. Pupo
- School
of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Jon Clardy
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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13
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Bae M, Mevers E, Pishchany G, Whaley SG, Rock CO, Andes DR, Currie CR, Pupo MT, Clardy J. Chemical Exchanges between Multilateral Symbionts. Org Lett 2021; 23:1648-1652. [PMID: 33591189 DOI: 10.1021/acs.orglett.1c00068] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein is a report on the molecular exchange occurring between multilateral symbiosis partners-a tit-for-tat exchange that led to the characterization of two new metabolites, conocandin B (fungal-derived) and dentigerumycin F (bacterial-derived). The structures were determined by NMR, mass spectrometry, genomic analysis, and chemical derivatizations. Conocandin B exhibits antimicrobial activity against both the bacterial symbionts of fungus-growing ant and human pathogenic strains by selectively inhibiting FabH, thus disrupting fatty acid biosynthesis.
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Affiliation(s)
- Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Gleb Pishchany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sarah G Whaley
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Monica T Pupo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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14
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Menegatti C, Fukuda TTH, Pupo MT. Chemical Ecology in Insect-microbe Interactions in the Neotropics. PLANTA MEDICA 2021; 87:38-48. [PMID: 32854122 DOI: 10.1055/a-1229-9435] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small molecules frequently mediate symbiotic interactions between microorganisms and their hosts. Brazil harbors the highest diversity of insects in the world; however, just recently, efforts have been directed to deciphering the chemical signals involved in the symbioses of microorganisms and social insects. The current scenario of natural products research guided by chemical ecology is discussed in this review. Two groups of social insects have been prioritized in the studies, fungus-farming ants and stingless bees, leading to the identification of natural products involved in defensive and nutritional symbioses. Some of the compounds also present potential pharmaceutical applications as antimicrobials, and this is likely related to their ecological roles. Microbial symbioses in termites and wasps are suggested promising sources of biologically active small molecules. Aspects related to public policies for insect biodiversity preservation are also highlighted.
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Affiliation(s)
- Carla Menegatti
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Taise T H Fukuda
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Mônica T Pupo
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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15
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Tao H, Zuo L, Xu H, Li C, Qiao G, Guo M, Lin X. Alkaloids as Anticancer Agents: A Review of Chinese Patents in Recent 5 Years. Recent Pat Anticancer Drug Discov 2021; 15:2-13. [PMID: 32003702 DOI: 10.2174/1574892815666200131120618] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/19/2020] [Accepted: 01/28/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND In recent years, many novel alkaloids with anticancer activity have been found in China, and some of them are promising for developing as anticancer agents. OBJECTIVE This review aims to provide a comprehensive overview of the information about alkaloid anticancer agents disclosed in Chinese patents, and discusses their potential to be developed as anticancer drugs used clinically. METHODS Anticancer alkaloids disclosed in Chinese patents in recent 5 years were presented according to their mode of actions. Their study results published on PubMed, and SciDirect databases were presented. RESULTS More than one hundred anticancer alkaloids were disclosed in Chinese patents and their mode of action referred to arresting cell cycle, inhibiting protein kinases, affecting DNA synthesis and p53 expression, etc. Conclusion: Many newly found alkaloids displayed potent anticancer activity both in vitro and in vivo, and some of the anticancer alkaloids acted as protein kinase inhibitors or CDK inhibitors possess the potential for developing as novel anticancer agents.
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Affiliation(s)
- Hongyu Tao
- Department of Pharmacology, School of Basic Medicine, Capital Medical University, Beijing 100069, China
| | - Ling Zuo
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan 646000, China
| | - Huanli Xu
- Department of Pharmacology, School of Basic Medicine, Capital Medical University, Beijing 100069, China
| | - Cong Li
- Department of Pharmacology, School of Basic Medicine, Capital Medical University, Beijing 100069, China
| | - Gan Qiao
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan 646000, China
| | - Mingyue Guo
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan 646000, China
| | - Xiukun Lin
- Department of Pharmacology, School of Pharmacy, Southwest Medical University, Sichuan 646000, China
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16
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Antileishmanial macrolides from ant-associated Streptomyces sp. ISID311. Bioorg Med Chem 2021; 32:116016. [PMID: 33493972 DOI: 10.1016/j.bmc.2021.116016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
Three antifungal macrolides cyphomycin (1), caniferolide C (2) and GT-35 (3) were isolated from Streptomyces sp. ISID311, a bacterial symbiont associated with Cyphomyrmex fungus-growing ants. The planar structures of these compounds were established by 1 and 2D NMR data and MS analysis. The relative configurations of 1-3 were established using Kishi's universal NMR database method, NOE/ROE analysis and coupling constants analysis assisted by comparisons with NMR data of related compounds. Detailed bioinformatic analysis of cyphomycin biosynthetic gene cluster confirmed the stereochemical assignments. Compounds 1-3 displayed high antagonism against different strains of Escovopsis sp., pathogen fungi specialized to the fungus-growing ant system. Compounds 1-3 also exhibited potent antiprotozoal activity against intracellular amastigotes of the human parasite Leishmania donovani with IC50 values of 2.32, 0.091 and 0.073 µM, respectively, with high selectivity indexes.
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17
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Goldstein SL, Klassen JL. Pseudonocardia Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism. Front Microbiol 2020; 11:621041. [PMID: 33424822 PMCID: PMC7793712 DOI: 10.3389/fmicb.2020.621041] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022] Open
Abstract
Actinobacteria belonging to the genus Pseudonocardia have evolved a close relationship with multiple species of fungus-growing ants, where these bacteria produce diverse secondary metabolites that protect the ants and their fungal mutualists from disease. Recent research has charted the phylogenetic diversity of this symbiosis, revealing multiple instances where the ants and Pseudonocardia have formed stable relationships in which these bacteria are housed on specific regions of the ant's cuticle. Parallel chemical and genomic analyses have also revealed that symbiotic Pseudonocardia produce diverse secondary metabolites with antifungal and antibacterial bioactivities, and highlighted the importance of plasmid recombination and horizontal gene transfer for maintaining these symbiotic traits. Here, we propose a multi-level model for the evolution of Pseudonocardia and their secondary metabolites that includes symbiont transmission within and between ant colonies, and the potentially independent movement and diversification of their secondary metabolite biosynthetic genes. Because of their well-studied ecology and experimental tractability, Pseudonocardia symbionts of fungus-growing ants are an especially useful model system to understand the evolution of secondary metabolites, and also comprise a significant source of novel antibiotic and antifungal agents.
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Affiliation(s)
- Sarah L Goldstein
- Department of Molecular and Cell Biology, University of Connecticut, Mansfield, CT, United States
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Mansfield, CT, United States
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18
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Batey SFD, Greco C, Hutchings MI, Wilkinson B. Chemical warfare between fungus-growing ants and their pathogens. Curr Opin Chem Biol 2020; 59:172-181. [PMID: 32949983 PMCID: PMC7763482 DOI: 10.1016/j.cbpa.2020.08.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022]
Abstract
Fungus-growing attine ants are under constant threat from fungal pathogens such as the specialized mycoparasite Escovopsis, which uses combined physical and chemical attack strategies to prey on the fungal gardens of the ants. In defence, some species assemble protective microbiomes on their exoskeletons that contain antimicrobial-producing Actinobacteria. Underlying this network of mutualistic and antagonistic interactions are an array of chemical signals. Escovopsis weberi produces the shearinine terpene-indole alkaloids, which affect ant behaviour, diketopiperazines to combat defensive bacteria, and other small molecules that inhibit the fungal cultivar. Pseudonocardia and Streptomyces mutualist bacteria produce depsipeptide and polyene macrolide antifungals active against Escovopsis spp. The ant nest metabolome is further complicated by competition between defensive bacteria, which produce antibacterials active against even closely related species. Specialist fungal pathogens attack the nests of fungus-growing ants. Ants form mutualistic relationships with defensive actinomycete bacteria. Specialised metabolites underpin these mutualistic and antagonistic interactions.
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Affiliation(s)
- Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Claudio Greco
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom; School of Biological Sciences, University of East Anglia, Norwich, NR4 7TU, United Kingdom.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, United Kingdom.
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19
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Zenkov RG, Ektova LV, Vlasova OА, Belitskiy GА, Yakubovskaya MG, Kirsanov KI. Indolo[2,3-a]carbazoles: diversity, biological properties, application in antitumor therapy. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02714-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Yang CL, Zhang B, Xue WW, Li W, Xu ZF, Shi J, Shen Y, Jiao RH, Tan RX, Ge HM. Discovery, Biosynthesis, and Heterologous Production of Loonamycin, a Potent Anticancer Indolocarbazole Alkaloid. Org Lett 2020; 22:4665-4669. [DOI: 10.1021/acs.orglett.0c01456] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cheng Long Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wen Wen Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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21
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Chang PT, Rao K, Longo LO, Lawton ES, Scherer G, Van Arnam EB. Thiopeptide Defense by an Ant's Bacterial Symbiont. JOURNAL OF NATURAL PRODUCTS 2020; 83:725-729. [PMID: 31961674 DOI: 10.1021/acs.jnatprod.9b00897] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fungus-growing ants and their microbial symbionts have emerged as a model system for understanding antibiotic deployment in an ecological context. Here we establish that bacterial symbionts of the ant Trachymyrmex septentrionalis antagonize their most likely competitors, other strains of ant-associated bacteria, using the thiopeptide antibiotic GE37468. Genomic analysis suggests that these symbionts acquired the GE37468 gene cluster from soil bacteria. This antibiotic, with known activity against human pathogens, was previously identified in a biochemical screen but had no known ecological role. GE37468's host-associated defense role in this insect niche intriguingly parallels the function of similar thiopeptides in the human microbiome.
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Affiliation(s)
- Preston T Chang
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Krithika Rao
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Lauren O Longo
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Elisabeth S Lawton
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Georgia Scherer
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Ethan B Van Arnam
- Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
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22
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Fukuda TTH, Cassilly CD, Gerdt JP, Henke MT, Helfrich EJN, Mevers E. Research Tales from the Clardy Laboratory: Function-Driven Natural Product Discovery. JOURNAL OF NATURAL PRODUCTS 2020; 83:744-755. [PMID: 32105475 DOI: 10.1021/acs.jnatprod.9b01086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past 70 years, the search for small molecules from nature has transformed biomedical research: natural products are the basis for half of all pharmaceuticals; the quest for total synthesis of natural products fueled development of methodologies for organic synthesis; and their biosynthesis presented unprecedented biochemical transformations, expanding our chemo-enzymatic toolkit. Initially, the discovery of small molecules was driven by bioactivity-guided fractionation. However, this approach yielded the frequent rediscovery of already known metabolites. As a result, focus shifted to identifying novel scaffolds through either structure-first methods or genome mining, relegating function as a secondary concern. Over the past two decades, the laboratory of Jon Clardy has taken an alternative route and focused on an ecology-driven, function-first approach in pursuit of uncovering bacterial small molecules with biological activity. In this review, we highlight several examples that showcase this ecology-first approach. Though the highlighted systems are diverse, unifying themes are (1) to understand how microbes interact with their host or environment, (2) to gain insights into the environmental roles of microbial metabolites, and (3) to explore pharmaceutical potential from these ecologically relevant metabolites.
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Affiliation(s)
- Taise T H Fukuda
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Chelsi D Cassilly
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Matthew T Henke
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eric J N Helfrich
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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23
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Ortega HE, Ferreira LLG, Melo WGP, Oliveira ALL, Ramos Alvarenga RF, Lopes NP, Bugni TS, Andricopulo AD, Pupo MT. Antifungal compounds from Streptomyces associated with attine ants also inhibit Leishmania donovani. PLoS Negl Trop Dis 2019; 13:e0007643. [PMID: 31381572 PMCID: PMC6695191 DOI: 10.1371/journal.pntd.0007643] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/15/2019] [Accepted: 07/19/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial strains isolated from attine ants showed activity against the insect specialized fungal pathogen Escovopsis and also against the human protozoan parasite Leishmania donovani. The bioassay guided fractionation of extracts from cultures of Streptomyces sp. ICBG292, isolated from the exoskeleton of Cyphomyrmex workers, led to the isolation of Mer-A2026B (1), piericidin-A1 (2) and nigericin (3). Nigericin (3) presented high activity against intracellular amastigotes of L. donovani (IC50 0.129 ± 0.008 μM). Streptomyces puniceus ICBG378, isolated from workers of Acromyrmex rugosus rugosus, produced dinactin (4) with potent anti-L. donovani activity against intracellular amastigotes (IC50 0.018 ± 0.003 μM). Compounds 3 and 4 showed good selectivity indexes, 88.91 and 656.11 respectively, and were more active than positive control, miltefosine. Compounds 1–4 were also active against some Escovopsis strains. Compounds 1 and 2 were also produced by Streptomyces sp. ICBG233, isolated from workers of Atta sexdens, and detected in ants’ extracts by mass spectrometry, suggesting they are produced in the natural environment as defensive compounds involved in the symbiotic interaction. Visceral leishmaniasis, caused by Leishmania infantum and L. donovani, is characterized by high rate mortality worldwide. Current treatments for this disease suffer from toxicity, variable efficacy, requirements for parenteral administration and length of treatment regimens. New chemical entities and development of new drugs are important to overcome the impact of this protozoan disease. Actinobacterial strains, such as Streptomyces, have been a source of most naturally derived antibiotics, as well as anticancer, anthelmintic, and antifungal drugs. These microorganisms also produce small molecules important in symbiotic interactions with insects, such as fungus-growing ants, fungus-growing termites, beetles and wasps against pathogens. Several novel compounds have been reported from these microorganisms with promising biological activities. In this work we show an interesting ecologic approach for drug discovery that also shows promise for the identification of antileishmanial natural products from fungus-growing ant ecosystem. Two compounds isolated from Streptomyces strains showed potent activity against L. donovani, higher than the positive control (miltefosine) with high selectivity indexes.
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Affiliation(s)
- Humberto E. Ortega
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Leonardo L. G. Ferreira
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
| | - Weilan G. P. Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ana Ligia L. Oliveira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - René F. Ramos Alvarenga
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Norberto P. Lopes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Adriano D. Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
| | - Mônica T. Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- * E-mail:
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24
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Janosik T, Rannug A, Rannug U, Wahlström N, Slätt J, Bergman J. Chemistry and Properties of Indolocarbazoles. Chem Rev 2018; 118:9058-9128. [PMID: 30191712 DOI: 10.1021/acs.chemrev.8b00186] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The indolocarbazoles are an important class of nitrogen heterocycles which has evolved significantly in recent years, with numerous studies focusing on their diverse biological effects, or targeting new materials with potential applications in organic electronics. This review aims at providing a broad survey of the chemistry and properties of indolocarbazoles from an interdisciplinary point of view, with particular emphasis on practical synthetic aspects, as well as certain topics which have not been previously accounted for in detail, such as the occurrence, formation, biological activities, and metabolism of indolo[3,2- b]carbazoles. The literature of the past decade forms the basis of the text, which is further supplemented with older key references.
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Affiliation(s)
- Tomasz Janosik
- Research Institutes of Sweden , Bioscience and Materials, RISE Surface, Process and Formulation , SE-151 36 Södertälje , Sweden
| | - Agneta Rannug
- Institute of Environmental Medicine , Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Ulf Rannug
- Department of Molecular Biosciences, The Wenner-Gren Institute , Stockholm University , SE-106 91 Stockholm , Sweden
| | | | - Johnny Slätt
- Department of Chemistry, Applied Physical Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Jan Bergman
- Karolinska Institutet , Department of Biosciences and Nutrition , SE-141 83 Huddinge , Sweden
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25
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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26
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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: 63] [Impact Index Per Article: 9.0] [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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27
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Pyrazines from bacteria and ants: convergent chemistry within an ecological niche. Sci Rep 2018; 8:2595. [PMID: 29416082 PMCID: PMC5803209 DOI: 10.1038/s41598-018-20953-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/26/2018] [Indexed: 02/07/2023] Open
Abstract
Ants use pheromones to coordinate their communal activity. Volatile pyrazines, for instance, mediate food resource gathering and alarm behaviors in different ant species. Here we report that leaf-cutter ant-associated bacteria produce a family of pyrazines that includes members previously identified as ant trail and alarm pheromones. We found that L-threonine induces the bacterial production of the trail pheromone pyrazines, which are common for the host leaf-cutter ants. Isotope feeding experiments revealed that L-threonine along with sodium acetate were the biosynthetic precursors of these natural products and a biosynthetic pathway was proposed.
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28
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Malmierca MG, González-Montes L, Pérez-Victoria I, Sialer C, Braña AF, García Salcedo R, Martín J, Reyes F, Méndez C, Olano C, Salas JA. Searching for Glycosylated Natural Products in Actinomycetes and Identification of Novel Macrolactams and Angucyclines. Front Microbiol 2018; 9:39. [PMID: 29441046 PMCID: PMC5797532 DOI: 10.3389/fmicb.2018.00039] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Many bioactive natural products are glycosylated compounds in which the sugar components usually participate in interaction and molecular recognition of the cellular target. Therefore, the presence of sugar moieties is important, in some cases essential, for bioactivity. Searching for novel glycosylated bioactive compounds is an important aim in the field of the research for natural products from actinomycetes. A great majority of these sugar moieties belong to the 6-deoxyhexoses and share two common biosynthetic steps catalyzed by a NDP-D-glucose synthase (GS) and a NDP-D-glucose 4,6-dehydratase (DH). Based on this fact, seventy one Streptomyces strains isolated from the integument of ants of the Tribe Attini were screened for the presence of biosynthetic gene clusters (BGCs) for glycosylated compounds. Total DNAs were analyzed by PCR amplification using oligo primers for GSs and DHs and also for a NDP-D-glucose-2,3-dehydratases. Amplicons were used in gene disruption experiments to generate non-producing mutants in the corresponding clusters. Eleven mutants were obtained and comparative dereplication analyses between the wild type strains and the corresponding mutants allowed in some cases the identification of the compound coded by the corresponding cluster (lobophorins, vicenistatin, chromomycins and benzanthrins) and that of two novel macrolactams (sipanmycin A and B). Several strains did not show UPLC differential peaks between the wild type strain and mutant profiles. However, after genome sequencing of these strains, the activation of the expression of two clusters was achieved by using nutritional and genetic approaches leading to the identification of compounds of the cervimycins family and two novel members of the warkmycins family. Our work defines a useful strategy for the identification new glycosylated compounds by a combination of genome mining, gene inactivation experiments and the activation of silent biosynthetic clusters in Streptomyces strains.
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Affiliation(s)
- Mónica G Malmierca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Lorena González-Montes
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | | | - Carlos Sialer
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Raúl García Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Jesús Martín
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
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29
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Van Arnam EB, Currie CR, Clardy J. Defense contracts: molecular protection in insect-microbe symbioses. Chem Soc Rev 2018; 47:1638-1651. [DOI: 10.1039/c7cs00340d] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Insects frequently host microbes that produce defensive molecules: a successful protective strategy and also an opportunity for antibiotic discovery
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Affiliation(s)
- Ethan B. Van Arnam
- Keck Science Department
- Claremont McKenna
- Pitzer
- and Scripps Colleges
- Claremont
| | | | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology
- Harvard Medical School
- Boston
- USA
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30
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Abstract
The small molecules produced by environmental bacteria have been mainstays of both chemical and biological research for decades, and some have led to important therapeutic interventions. These small molecules have been shaped by natural selection as they evolved to fulfill changing functional roles in their native environments. This minireview describes some recent systematic studies providing illustrative examples that involve the acquisition and alteration of genetic information for molecular innovation by bacteria in well-defined environments. Two different bacterial genera are featured, Pseudonocardia and Salinispora, and, although the small-molecule repertoires of both have benefited from horizontal gene transfer, Pseudonocardia spp. have relied on plasmid-based tactics while Salinispora spp. have relied on chromosomally integrated genomic islands.
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Affiliation(s)
- Antonio C Ruzzini
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Molloy EM, Hertweck C. Antimicrobial discovery inspired by ecological interactions. Curr Opin Microbiol 2017; 39:121-127. [PMID: 29169087 DOI: 10.1016/j.mib.2017.09.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023]
Abstract
Bacteria represent an unparalleled source of antibiotics used to treat infectious diseases. Yet, genome analyses have revealed that their full biosynthetic potential is much larger than expected. Valuable strategies to unearth hidden antibiotics are genome mining, pathway engineering and triggering, as well as co-cultivation approaches. Nevertheless, there is growing understanding that it is often essential to consider the ecological context and that there is a great potential for antimicrobial discovery from bacteria engaged in well-defined interactions with other organisms. Various ecological scenarios involving antimicrobial agents are outlined in this review: predator-prey and pathogenic interactions, the protection of insect assets such as offspring and cultivars, as well as host protection in symbiotic relationships with plants, invertebrates and animals/humans. The illustrative examples given reinforce the idea that examination of interactions between organisms can yield new antimicrobial compounds, and ultimately further our understanding of the function of these molecules in the environment.
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Affiliation(s)
- Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany; Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany.
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32
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Wyche TP, Ruzzini AC, Schwab L, Currie CR, Clardy J. Tryptorubin A: A Polycyclic Peptide from a Fungus-Derived Streptomycete. J Am Chem Soc 2017; 139:12899-12902. [PMID: 28853867 PMCID: PMC5609116 DOI: 10.1021/jacs.7b06176] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Fungus-growing ants engage in complex
symbiotic relationships with
their fungal crop, specialized fungal pathogens, and bacteria that
provide chemical defenses. In an effort to understand the evolutionary
origins of this multilateral system, we investigated bacteria isolated
from fungi. One bacterial strain (Streptomyces sp. CLI2509) from the bracket fungus Hymenochaete
rubiginosa, produced an unusual peptide, tryptorubin
A, which contains heteroaromatic links between side chains that give
it a rigid polycyclic globular structure. The three-dimensional structure
was determined by NMR and MS, including a 13C-13C COSY of isotopically enriched material, degradation, derivatives,
and computer modeling. Whole genome sequencing identified a likely
pair of biosynthetic genes responsible for tryptorubin A’s
linear hexapeptide backbone. The genome also revealed the close relationship
between CLI2509 and Streptomyces sp.
SPB78, which was previously implicated in an insect–bacterium
symbiosis.
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Affiliation(s)
- Thomas P Wyche
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Antonio C Ruzzini
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Laura Schwab
- Department of Bacteriology, University of Wisconsin-Madison , 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison , 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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33
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Abstract
Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.
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Affiliation(s)
- Navid Adnani
- University of Wisconsin Madison, School of Pharmacy, Div. of Pharmaceutical Sciences, 777 Highland Ave., Madison, WI 53705-2222, USA.
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34
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Baskin JM, Aye Y. Meeting Proceedings, 2017 Cornell University Baker Symposium-Quo Vadis: The Boundless Trajectories of Chemical Biology. Biochemistry 2017; 56:2967-2970. [PMID: 28558237 DOI: 10.1021/acs.biochem.7b00495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Weill Institute for Cell and Molecular Biology, Cornell University , Ithaca, New York 14853, United States
| | - Yimon Aye
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Department of Biochemistry, Weill Cornell Medicine , New York, New York 10065, United States
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35
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Baskin JM, Aye Y. Meeting Proceedings, 2017 Cornell University Baker Symposium— Quo Vadis: The Boundless Trajectories of Chemical Biology. ACS Chem Biol 2017. [DOI: 10.1021/acschembio.7b00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeremy M. Baskin
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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36
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Asamizu S. Biosynthesis of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles, from actinomycetes. Biosci Biotechnol Biochem 2017; 81:871-881. [DOI: 10.1080/09168451.2017.1281726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles. Validamycin A is a member of C7N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C7-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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37
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Behie SW, Bonet B, Zacharia VM, McClung DJ, Traxler MF. Molecules to Ecosystems: Actinomycete Natural Products In situ. Front Microbiol 2017; 7:2149. [PMID: 28144233 PMCID: PMC5239776 DOI: 10.3389/fmicb.2016.02149] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/20/2016] [Indexed: 11/13/2022] Open
Abstract
Actinomycetes, filamentous actinobacteria found in numerous ecosystems around the globe, produce a wide range of clinically useful natural products (NP). In natural environments, actinomycetes live in dynamic communities where environmental cues and ecological interactions likely influence NP biosynthesis. Our current understating of these cues, and the ecological roles of NP, is in its infancy. We postulate that understanding the ecological context in which actinomycete metabolites are made is fundamental to advancing the discovery of novel NP. In this review we explore the ecological relevance of actinomycetes and their secondary metabolites from varying ecosystems, and suggest that investigating the ecology of actinomycete interactions warrants particular attention with respect to metabolite discovery. Furthermore, we focus on the chemical ecology and in situ analysis of actinomycete NP and consider the implications for NP biosynthesis at ecosystem scales.
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Affiliation(s)
- Scott W Behie
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Bailey Bonet
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Vineetha M Zacharia
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Dylan J McClung
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley CA, USA
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38
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Selvamicin, an atypical antifungal polyene from two alternative genomic contexts. Proc Natl Acad Sci U S A 2016; 113:12940-12945. [PMID: 27803316 DOI: 10.1073/pnas.1613285113] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacteria harbored by fungus-growing ants produce a variety of small molecules that help maintain a complex multilateral symbiosis. In a survey of antifungal compounds from these bacteria, we discovered selvamicin, an unusual antifungal polyene macrolide, in bacterial isolates from two neighboring ant nests. Selvamicin resembles the clinically important antifungals nystatin A1 and amphotericin B, but it has several distinctive structural features: a noncationic 6-deoxymannose sugar at the canonical glycosylation site and a second sugar, an unusual 4-O-methyldigitoxose, at the opposite end of selvamicin's shortened polyene macrolide. It also lacks some of the pharmacokinetic liabilities of the clinical agents and appears to have a different target. Whole genome sequencing revealed the putative type I polyketide gene cluster responsible for selvamicin's biosynthesis including a subcluster of genes consistent with selvamicin's 4-O-methyldigitoxose sugar. Although the selvamicin biosynthetic cluster is virtually identical in both bacterial producers, in one it is on the chromosome, in the other it is on a plasmid. These alternative genomic contexts illustrate the biosynthetic gene cluster mobility that underlies the diversity and distribution of chemical defenses by the specialized bacteria in this multilateral symbiosis.
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39
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Beuzer P, La Clair JJ, Cang H. Color-Coded Super-Resolution Small-Molecule Imaging. Chembiochem 2016; 17:999-1003. [PMID: 26994590 PMCID: PMC5291120 DOI: 10.1002/cbic.201600013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 12/15/2022]
Abstract
Although the development of super-resolution microscopy dates back to 1994, its applications have been primarily focused on visualizing cellular structures and targets, including proteins, DNA and sugars. We now report on a system that allows both monitoring of the localization of exogenous small molecules in live cells at low resolution and subsequent super-resolution imaging by using stochastic optical reconstruction microscopy (STORM) on fixed cells. This represents a powerful new tool to understand the dynamics of subcellular trafficking associated with the mode and mechanism of action of exogenous small molecules.
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Affiliation(s)
- Paolo Beuzer
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James J La Clair
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1052, USA.
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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40
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Abstract
A personal selection of 33 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as pseudellone A from Pseudallescheria ellipsoidea.
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