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Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024:e0060024. [PMID: 38771054 DOI: 10.1128/aem.00600-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
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Affiliation(s)
- Christopher P Harper
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Joshua A V Blodgett
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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Ashraf N, Anas A, Sukumaran V, Gopinath G, Idrees Babu KK, Dinesh Kumar PK. Recent advancements in coral health, microbiome interactions and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163085. [PMID: 36996987 DOI: 10.1016/j.scitotenv.2023.163085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/13/2023]
Abstract
Corals are the visible indicators of the disasters induced by global climate change and anthropogenic activities and have become a highly vulnerable ecosystem on the verge of extinction. Multiple stressors could act individually or synergistically which results in small to large scale tissue degradation, reduced coral covers, and makes the corals vulnerable to various diseases. The coralline diseases are like the Chicken pox in humans because they spread hastily throughout the coral ecosystem and can devastate the coral cover formed over centuries in an abbreviated time. The extinction of the entire reef ecosystem will alter the ocean and earth's amalgam of biogeochemical cycles causing a threat to the entire planet. The current manuscript provides an overview of the recent advancement in coral health, microbiome interactions and climate change. Culture dependent and independent approaches in studying the microbiome of corals, the diseases caused by microorganisms, and the reservoirs of coral pathogens are also discussed. Finally, we discuss the possibilities of protecting the coral reefs from diseases through microbiome transplantation and the capabilities of remote sensing in monitoring their health status.
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Affiliation(s)
- Nizam Ashraf
- CSIR - National Institute of Oceanography, Regional Centre, Kochi 682018, India
| | - Abdulaziz Anas
- CSIR - National Institute of Oceanography, Regional Centre, Kochi 682018, India.
| | - Vrinda Sukumaran
- CSIR - National Institute of Oceanography, Regional Centre, Kochi 682018, India
| | - Girish Gopinath
- Department of Climate Variability and Aquatic Ecosystems, Kerala University of Fisheries and Ocean Studies (KUFOS), Puduvypu Campus, Kochi 682 508, India
| | - K K Idrees Babu
- Department of Science and Technology, Kavaratti, Lakshadweep 682555, India
| | - P K Dinesh Kumar
- CSIR - National Institute of Oceanography, Regional Centre, Kochi 682018, India
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Sarmiento-Vizcaíno A, Martín J, Ortiz-López FJ, Reyes F, García LA, Blanco G. Natural products, including a new caboxamycin, from Streptomyces and other Actinobacteria isolated in Spain from storm clouds transported by Northern winds of Arctic origin. Front Chem 2022; 10:948795. [DOI: 10.3389/fchem.2022.948795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Actinobacteria, mostly Streptomyces species, are the main source of natural products essential in medicine. While the majority of producer microorganisms of secondary metabolite are reported from terrestrial or marine environments, there are limited reports of their isolation from atmospheric precipitations. Clouds are considered as atmospheric oases for microorganisms and there is a recent paradigm shift whereby atmospheric-derived Actinobacteria emerge as an alternative source for drug discovery. In this context, we studied a total of 18 bioactive Actinobacteria strains, isolated by sampling nine precipitation events with prevailing Northern winds in the Cantabrian Sea coast, Northern Spain. Backward trajectories meteorological analyses indicate that air masses were originated mostly in the Arctic Ocean, and their trajectory to downwind areas involved the Atlantic Ocean and also terrestrial sources from continental Europe, and in some events from Canada, Greenland, Mauritania and Canary Islands. Taxonomic identification of the isolates, by 16S rRNA gene sequencing and phylogenetic analyses, revealed that they are members of three Actinobacteria genera. Fifteen of the isolates are Streptomyces species, thus increasing the number of bioactive species of this genus in the atmosphere to a 6.8% of the total currently validated species. In addition, two of the strains belong to the genus Micromonospora and one to genus Nocardiopsis. These findings reinforce a previous atmospheric dispersal model, extended herein to the genus Micromonospora. Production of bioactive secondary metabolites was screened in ethyl acetate extracts of the strains by LC-UV-MS and a total of 94 secondary metabolites were detected after LC/MS dereplication. Comparative analyses with natural products databases allowed the identification of 69 structurally diverse natural products with contrasted biological activities, mostly as antibiotics and antitumor agents, but also anti-inflammatory, antiviral, antiparasitic, immunosuppressant and neuroprotective among others. The molecular formulae of the 25 remaining compounds were determined by HRMS. None of these molecules had been previously reported in natural product databases indicating potentially novel metabolites. As a proof of concept, a new metabolite caboxamycin B (1) was isolated from the culture broth of Streptomyces sp. A-177 and its structure was determined by various spectrometric methods. To the best of our knowledge, this is the first novel natural product obtained from an atmospheric Streptomyces, thus pointing out precipitations as an innovative source for discovering new pharmaceutical natural products.
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Alviz-Gazitua P, González A, Lee MR, Aranda CP. Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:431-447. [PMID: 35486299 DOI: 10.1007/s10126-022-10097-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.
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Affiliation(s)
- P Alviz-Gazitua
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - A González
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile
| | - M R Lee
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue km 6, P. Box 5480000, Puerto Montt, Chile
| | - C P Aranda
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avda. Fuchslocher 1305, P. Box 5290000, Osorno, Chile.
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Deutsch JM, Mandelare-Ruiz P, Yang Y, Foster G, Routhu A, Houk J, De La Flor YT, Ushijima B, Meyer JL, Paul VJ, Garg N. Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria. JOURNAL OF NATURAL PRODUCTS 2022; 85:462-478. [PMID: 35112871 DOI: 10.1021/acs.jnatprod.1c01110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.
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Affiliation(s)
- Jessica M Deutsch
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Paige Mandelare-Ruiz
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Yingzhe Yang
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gabriel Foster
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurva Routhu
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jay Houk
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Yesmarie T De La Flor
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Blake Ushijima
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - Julie L Meyer
- Department of Soil and Water Sciences, University of Florida, Gainesville, Florida 32603, United States
| | - Valerie J Paul
- Smithsonian Marine Station, Smithsonian Institution, Fort Pierce, Florida 34949, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Engineered Biosystems Building, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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Li H, Fang X, qiangjun S, yinxia X, gang Z, Zhaohe C. Transcriptome analysis the effects of light treatment on Ophiocordyceps sinensis metabolism. Int J Med Mushrooms 2022; 24:81-97. [DOI: 10.1615/intjmedmushrooms.2022044445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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10
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Sarmiento-Vizcaíno A, Martín J, Reyes F, García LA, Blanco G. Bioactive Natural Products in Actinobacteria Isolated in Rainwater From Storm Clouds Transported by Western Winds in Spain. Front Microbiol 2021; 12:773095. [PMID: 34858379 PMCID: PMC8631523 DOI: 10.3389/fmicb.2021.773095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are the main producers of bioactive natural products essential for human health. Although their diversity in the atmosphere remains largely unexplored, using a multidisciplinary approach, we studied here 27 antibiotic producing Actinobacteria strains, isolated from 13 different precipitation events at three locations in Northern and Southern Spain. Rain samples were collected throughout 2013-2016, from events with prevailing Western winds. NOAA HYSPLIT meteorological analyses were used to estimate the sources and trajectories of the air-mass that caused the rainfall events. Five-day backward air masses trajectories of the diverse events reveals a main oceanic source from the North Atlantic Ocean, and in some events long range transport from the Pacific and the Arctic Oceans; terrestrial sources from continental North America and Western Europe were also estimated. Different strains were isolated depending on the precipitation event and the latitude of the sampling site. Taxonomic identification by 16S rRNA sequencing and phylogenetic analysis revealed these strains to belong to two Actinobacteria genera. Most of the isolates belong to the genus Streptomyces, thus increasing the number of species of this genus isolated from the atmosphere. Furthermore, five strains belonging to the rare Actinobacterial genus Nocardiopsis were isolated in some events. These results reinforce our previous Streptomyces atmospheric dispersion model, which we extend herein to the genus Nocardiopsis. Production of bioactive secondary metabolites was analyzed by LC-UV-MS. Comparative analyses of Streptomyces and Nocardiopsis metabolites with natural product databases led to the identification of multiple, chemically diverse, compounds. Among bioactive natural products identified 55% are antibiotics, both antibacterial and antifungal, and 23% have antitumor or cytotoxic properties; also compounds with antiparasitic, anti-inflammatory, immunosuppressive, antiviral, insecticidal, neuroprotective, anti-arthritic activities were found. Our findings suggest that over time, through samples collected from different precipitation events, and space, in different sampling places, we can have access to a great diversity of Actinobacteria producing an extraordinary reservoir of bioactive natural products, from remote and very distant origins, thus highlighting the atmosphere as a contrasted source for the discovery of novel compounds of relevance in medicine and biotechnology.
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Affiliation(s)
- Aida Sarmiento-Vizcaíno
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Universidad de Oviedo, Oviedo, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada, Spain
| | - Luis A García
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Área de Ingeniería Química, Universidad de Oviedo, Oviedo, Spain
| | - Gloria Blanco
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Universidad de Oviedo, Oviedo, Spain
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Singh R, Chauhan N, Kuddus M. Exploring the therapeutic potential of marine-derived bioactive compounds against COVID-19. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:52798-52809. [PMID: 34476696 PMCID: PMC8412857 DOI: 10.1007/s11356-021-16104-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
The ocean is the most biodiverse habitat of various organisms. The organisms surviving in the harsh conditions of the ocean consist of several spectacular properties and produce bioactive compounds of pharmacological importance. These compounds are effective even in small quantities with various immunomodulatory qualities such as antioxidant and anti-inflammatory properties. Though the vaccines for COVID-19 are developed, and drug development is also in progress, but till now no effective drug is available for this deadly virus. Researchers are mining the huge data of bioactive compounds to develop the specific drug for COVID-19. The use of the repurposed drugs is challenging against the rapidly mutating virus with variable symptoms and mode of transmission. This review is an attempt to compile all the spattered data of marine-derived bioactive compounds with antiviral properties and to explore their therapeutic potential against COVID-19.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Uttar Pradesh, 226028, India.
| | - Niketa Chauhan
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, Uttar Pradesh, 226028, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Saudi Arabia
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Ding W, Tu J, Zhang H, Wei X, Ju J, Li Q. Genome Mining and Metabolic Profiling Uncover Polycyclic Tetramate Macrolactams from Streptomyces koyangensis SCSIO 5802. Mar Drugs 2021; 19:md19080440. [PMID: 34436279 PMCID: PMC8399814 DOI: 10.3390/md19080440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
We have previously shown deep-sea-derived Streptomyces koyangensis SCSIO 5802 to produce two types of active secondary metabolites, abyssomicins and candicidins. Here, we report the complete genome sequence of S. koyangensis SCSIO 5802 employing bioinformatics to highlight its potential to produce at least 21 categories of natural products. In order to mine novel natural products, the production of two polycyclic tetramate macrolactams (PTMs), the known 10-epi-HSAF (1) and a new compound, koyanamide A (2), was stimulated via inactivation of the abyssomicin and candicidin biosynthetic machineries. Detailed bioinformatics analyses revealed a PKS/NRPS gene cluster, containing 6 open reading frames (ORFs) and spanning ~16 kb of contiguous genomic DNA, as the putative PTM biosynthetic gene cluster (BGC) (termed herein sko). We furthermore demonstrate, via gene disruption experiments, that the sko cluster encodes the biosynthesis of 10-epi-HSAF and koyanamide A. Finally, we propose a plausible biosynthetic pathway to 10-epi-HSAF and koyanamide A. In total, this study demonstrates an effective approach to cryptic BGC activation enabling the discovery of new bioactive metabolites; genome mining and metabolic profiling methods play key roles in this strategy.
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Affiliation(s)
- Wenjuan Ding
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Tu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
| | - Huaran Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China;
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- College of Oceanology, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510301, China
- Correspondence: (J.J.); (Q.L.); Tel.: +86-20-8902-3028 (J.J. & Q.L.)
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (J.T.); (H.Z.)
- Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510301, China
- Correspondence: (J.J.); (Q.L.); Tel.: +86-20-8902-3028 (J.J. & Q.L.)
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Michán C, Blasco J, Alhama J. High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microb Biotechnol 2021; 14:870-885. [PMID: 33559398 PMCID: PMC8085945 DOI: 10.1111/1751-7915.13763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
| | - Julián Blasco
- Department of Ecology and Coastal ManagementICMAN‐CSICCampus Rio San PedroPuerto Real (Cádiz)E‐11510Spain
| | - José Alhama
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
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Keller-Costa T, Lago-Lestón A, Saraiva JP, Toscan R, Silva SG, Gonçalves J, Cox CJ, Kyrpides N, Nunes da Rocha U, Costa R. Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals. MICROBIOME 2021; 9:72. [PMID: 33766108 PMCID: PMC7993494 DOI: 10.1186/s40168-021-01031-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. RESULTS Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system. CONCLUSIONS This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.
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Affiliation(s)
- T. Keller-Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - A. Lago-Lestón
- División de Biología Experimental y Aplicada (DBEA), Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carr. Ensenada-Tijuana 3918, Zona Playitas, C.P 22860 Ensenada, Baja California Mexico
| | - J. P. Saraiva
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Toscan
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - S. G. Silva
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
| | - J. Gonçalves
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - C. J. Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
| | - N. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
| | - U. Nunes da Rocha
- Helmholtz Centre for Environmental Research (UFZ), Leipzig, 04318 Germany
| | - R. Costa
- Instituto de Bioengenharia e Biociências (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisbon, Portugal
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720 USA
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15
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A Pseudoalteromonas Clade with Remarkable Biosynthetic Potential. Appl Environ Microbiol 2021; 87:AEM.02604-20. [PMID: 33397702 DOI: 10.1128/aem.02604-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/19/2020] [Indexed: 02/02/2023] Open
Abstract
Pseudoalteromonas species produce a diverse range of biologically active compounds, including those biosynthesized by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). Here, we report the biochemical and genomic analysis of Pseudoalteromonas sp. strain HM-SA03, isolated from the blue-ringed octopus, Hapalochlaena sp. Genome mining for secondary metabolite pathways revealed seven putative NRPS/PKS biosynthesis gene clusters, including those for the biosynthesis of alterochromides, pseudoalterobactins, alteramides, and four novel compounds. Among these was a novel siderophore biosynthesis gene cluster with unprecedented architecture (NRPS-PKS-NRPS-PKS-NRPS-PKS-NRPS). Alterochromide production in HM-SA03 was also confirmed by liquid chromatography-mass spectrometry. An investigation of the biosynthetic potential of 42 publicly available Pseudoalteromonas genomes indicated that some of these gene clusters are distributed throughout the genus. Through the phylogenetic analysis, a particular subset of strains formed a clade with extraordinary biosynthetic potential, with an average density of 10 biosynthesis gene clusters per genome. In contrast, the majority of Pseudoalteromonas strains outside this clade contained an average of three clusters encoding complex biosynthesis. These results highlight the underexplored potential of Pseudoalteromonas as a source of new natural products.IMPORTANCE This study demonstrates that the Pseudoalteromonas strain HM-SA03, isolated from the venomous blue-ringed octopus, Hapalochalaena sp., is a biosynthetically talented organism, capable of producing alterochromides and potentially six other specialized metabolites. We identified a pseudoalterobactin biosynthesis gene cluster and proposed a pathway for the production of the associated siderophore. A novel siderophore biosynthesis gene cluster with unprecedented architecture was also identified in the HM-SA03 genome. Finally, we demonstrated that HM-SA03 belongs to a phylogenetic clade of strains with extraordinary biosynthetic potential. While our results do not support a role of HM-SA03 in Hapalochalaena sp. venom (tetrodotoxin) production, they emphasize the untapped potential of Pseudoalteromonas as a source of novel natural products.
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16
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Pessotti RDC, Hansen BL, Reaso JN, Ceja-Navarro JA, El-Hifnawi L, Brodie EL, Traxler MF. Multiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North America. eLife 2021; 10:65091. [PMID: 33942718 PMCID: PMC8096431 DOI: 10.7554/elife.65091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
Some insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these associations, and how these strategies relate to insect lifestyle, remains underexplored. We assessed subsocial passalid beetles of the species Odontotaenius disjunctus, and their frass (fecal material), which is an important food resource within their galleries, as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus frass collected across eastern North America harbored multiple lineages of Streptomyces and diverse antimicrobials. Metabolites detected in frass displayed synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. These findings support a model in which the lifestyle of O. disjunctus accommodates multiple Streptomyces lineages in their frass, resulting in a rich repertoire of antimicrobials that likely insulates their galleries against pathogenic invasion.
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Affiliation(s)
- Rita de Cassia Pessotti
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Bridget L Hansen
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jewel N Reaso
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Javier A Ceja-Navarro
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States,Institute for Biodiversity Science and Sustainability, California Academy of SciencesBerkeleyUnited States
| | - Laila El-Hifnawi
- Department of Molecular and Cellular Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eoin L Brodie
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyUnited States,Department of Environmental Science, Policy and Management, University of California, BerkeleyBerkeleyUnited States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
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17
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Characterization of Actinomycetes Strains Isolated from the Intestinal Tract and Feces of the Larvae of the Longhorn Beetle Cerambyx welensii. Microorganisms 2020; 8:microorganisms8122013. [PMID: 33339339 PMCID: PMC7766275 DOI: 10.3390/microorganisms8122013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 01/06/2023] Open
Abstract
Actinomycetes constitute a large group of Gram-positive bacteria present in different habitats. One of these habitats involves the association of these bacteria with insects. In this work, we have studied twenty-four actinomycetes strains isolated from the intestinal tract and feces from larvae of the xylophagous coleopteran Cerambyx welensii and have shown that seventeen strains present hydrolytic activity of some of the following substrates: cellulose, hemicellulose, starch and proteins. Fourteen of the isolates produce antimicrobial molecules against the Gram-positive bacteria Micrococcus luteus. Analysis of seven strains led us to identify the production of a wide number of compounds including streptanoate, alpiniamide A, alteramides A and B, coproporphyrin III, deferoxamine, demethylenenocardamine, dihydropicromycin, nocardamine, picromycin, surugamides A, B, C, D and E, tirandamycins A and B, and valinomycin. A significant number of other compounds, whose molecular formulae are not included in the Dictionary of Natural Products (DNP), were also present in the extracts analyzed, which opens up the possibility of identifying new active antibiotics. Molecular identification of ten of the isolated bacteria determined that six of them belong to the genus Streptomyces, two of them are included in the genus Amycolatopsis and two in the genus Nocardiopsis.
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Bioactivity Potential of Marine Natural Products from Scleractinia-Associated Microbes and In Silico Anti-SARS-COV-2 Evaluation. Mar Drugs 2020; 18:md18120645. [PMID: 33339096 PMCID: PMC7765564 DOI: 10.3390/md18120645] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Marine organisms and their associated microbes are rich in diverse chemical leads. With the development of marine biotechnology, a considerable number of research activities are focused on marine bacteria and fungi-derived bioactive compounds. Marine bacteria and fungi are ranked on the top of the hierarchy of all organisms, as they are responsible for producing a wide range of bioactive secondary metabolites with possible pharmaceutical applications. Thus, they have the potential to provide future drugs against challenging diseases, such as cancer, a range of viral diseases, malaria, and inflammation. This review aims at describing the literature on secondary metabolites that have been obtained from Scleractinian-associated organisms including bacteria, fungi, and zooxanthellae, with full coverage of the period from 1982 to 2020, as well as illustrating their biological activities and structure activity relationship (SAR). Moreover, all these compounds were filtered based on ADME analysis to determine their physicochemical properties, and 15 compounds were selected. The selected compounds were virtually investigated for potential inhibition for SARS-CoV-2 targets using molecular docking studies. Promising potential results against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and methyltransferase (nsp16) are presented.
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19
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Atencio LA, Boya P. CA, Martin H. C, Mejía LC, Dorrestein PC, Gutiérrez M. Genome Mining, Microbial Interactions, and Molecular Networking Reveals New Dibromoalterochromides from Strains of Pseudoalteromonas of Coiba National Park-Panama. Mar Drugs 2020; 18:md18090456. [PMID: 32899199 PMCID: PMC7551054 DOI: 10.3390/md18090456] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 01/20/2023] Open
Abstract
The marine bacterial genus Pseudoalteromonas is known for their ability to produce antimicrobial compounds. The metabolite-producing capacity of Pseudoalteromonas has been associated with strain pigmentation; however, the genomic basis of their antimicrobial capacity remains to be explained. In this study, we sequenced the whole genome of six Pseudoalteromonas strains (three pigmented and three non-pigmented), with the purpose of identifying biosynthetic gene clusters (BGCs) associated to compounds we detected via microbial interactions along through MS-based molecular networking. The genomes were assembled and annotated using the SPAdes and RAST pipelines and mined for the identification of gene clusters involved in secondary metabolism using the antiSMASH database. Nineteen BGCs were detected for each non-pigmented strain, while more than thirty BGCs were found for two of the pigmented strains. Among these, the groups of genes of nonribosomal peptide synthetases (NRPS) that code for bromoalterochromides stand out the most. Our results show that all strains possess BGCs for the production of secondary metabolites, and a considerable number of distinct polyketide synthases (PKS) and NRPS clusters are present in pigmented strains. Furthermore, the molecular networking analyses revealed two new molecules produced during microbial interactions: the dibromoalterochromides D/D' (11-12).
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Affiliation(s)
- Librada A. Atencio
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Cristopher A. Boya P.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Christian Martin H.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Smithsonian Tropical Research Institute, Balboa Ancón, Panama City 0843-03092, Panama
- Correspondence: (L.C.M.); (M.G.); Tel.: +507-517-0700 (L.C.M. & M.G.); Fax: +507-517-0701 (L.C.M. & M.G.)
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA;
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT), Clayton, Panama City 0843-01103, Panama; (L.A.A.); (C.A.B.P.); (C.M.H.)
- Correspondence: (L.C.M.); (M.G.); Tel.: +507-517-0700 (L.C.M. & M.G.); Fax: +507-517-0701 (L.C.M. & M.G.)
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Ronai I, Greslehner GP, Boem F, Carlisle J, Stencel A, Suárez J, Bayir S, Bretting W, Formosinho J, Guerrero AC, Morgan WH, Prigot-Maurice C, Rodeck S, Vasse M, Wallis JM, Zacks O. "Microbiota, symbiosis and individuality summer school" meeting report. MICROBIOME 2020; 8:117. [PMID: 32795355 PMCID: PMC7427737 DOI: 10.1186/s40168-020-00898-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/24/2020] [Indexed: 05/13/2023]
Abstract
How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.
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Affiliation(s)
- Isobel Ronai
- Columbia University, 1200 Amsterdam Ave, New York, 10027 NY USA
| | - Gregor P. Greslehner
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076 France
| | - Federico Boem
- Dipartimento di Filosofia e Scienze dell’Educazione, Università degli Studi di Torino, Palazzo Nuovo, Via Sant’Ottavio, 20, Torino, 10124 Italy
| | - Judith Carlisle
- Washington University in St. Louis, Department of Philosophy, One Brookings Drive, St. Louis, 63130-4899 MO USA
| | - Adrian Stencel
- Institute of Philosophy, Jagiellonian University, Grodzka 52, Kraków, 33-332 Poland
| | - Javier Suárez
- Abteilung Philosophie, Universität Bielefeld, Universitätsstraße 25, Bielefeld, 33615 Germany
| | - Saliha Bayir
- Institut für Philosophie,Universität Kassel, Henschelstr. 2, Kassel, 34127 Germany
| | - Wiebke Bretting
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076 France
| | - Joana Formosinho
- Medical Museion, Department of Public Health, University of Copenhagen, Fredericiagade 18, Copenhagen, 1310 Denmark
| | - Anna C. Guerrero
- Arizona State University, Center for Biology and Society, 427 E Tyler Mall, Tempe, 85281 AZ USA
| | - William H. Morgan
- The University of Sheffield, Department of Philosophy, 45 Victoria Street, Sheffield, S3 7QB UK
| | - Cybèle Prigot-Maurice
- Université de Poitiers, Laboratoire Écologie et Biologie des Interactions, UMR CNRS 7267, Bâtiment B35, 5 rue Albert Turpain, TSA 51106, Poitiers Cedex 9, 86073 France
| | - Salome Rodeck
- Leibniz Center for Literary and Cultural Research, Schützenstr. 18, Berlin, 10117 Germany
| | - Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, 8092 Switzerland
| | - Jacqueline M. Wallis
- University of Bristol, Department of Philosophy, Cotham House, Bristol, BS6 6JL UK
| | - Oryan Zacks
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801 Israel
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21
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Coral Disease Causes, Consequences, and Risk within Coral Restoration. Trends Microbiol 2020; 28:793-807. [PMID: 32739101 DOI: 10.1016/j.tim.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022]
Abstract
As a result of increased reef degradation, restoration efforts are now being widely applied on coral reefs. However, outplanted coral survival in restoration zones varies substantially, and coral mortality can be a significant limitation to the success of restoration efforts. With reef restoration now occurring within, and adjacent to, nationally preserved and managed marine parks, the potential risks of mortality events and disease spread to adjacent marine populations need to be considered, particularly as these ecosystems continue to decline. We review the causes and consequences of coral mortality and disease outbreaks within the context of coral restoration, highlighting knowledge gaps in our understanding of the restored coral microbiome and discussing management practices for assessing coral disease. We identify the need for research efforts into monitoring and diagnostics of disease within coral restoration, as well as practices to mitigate and manage coral disease risks in restoration.
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22
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Hawaiian Bobtail Squid Symbionts Inhibit Marine Bacteria via Production of Specialized Metabolites, Including New Bromoalterochromides BAC-D/D'. mSphere 2020; 5:5/4/e00166-20. [PMID: 32611694 PMCID: PMC7333567 DOI: 10.1128/msphere.00166-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds. The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with >95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment. IMPORTANCE Animals that deposit eggs must protect their embryos from fouling and disease by microorganisms to ensure successful development. Although beneficial bacteria are hypothesized to contribute to egg defense in many organisms, the mechanisms of this protection are only recently being elucidated. Our previous studies of the Hawaiian bobtail squid focused on fungal inhibition by beneficial bacterial symbionts of a female reproductive gland and eggs. Herein, using genomic and chemical analyses, we demonstrate that symbiotic bacteria from this gland can also inhibit other marine bacteria in vitro. One bacterial strain in particular, Pseudoalteromonas sp. JC28, had broad-spectrum abilities to inhibit potential fouling bacteria, in part via production of novel bromoalterochromide metabolites, confirmed via genomic annotation of the associated biosynthetic gene cluster. Our results suggest that these bacterial metabolites may contribute to antimicrobial activity in this association and that such defensive symbioses are underutilized sources for discovering novel antimicrobial compounds.
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23
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The Biological and Chemical Diversity of Tetramic Acid Compounds from Marine-Derived Microorganisms. Mar Drugs 2020; 18:md18020114. [PMID: 32075282 PMCID: PMC7074263 DOI: 10.3390/md18020114] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022] Open
Abstract
Tetramic acid (pyrrolidine-2,4-dione) compounds, isolated from a variety of marine and terrestrial organisms, have attracted considerable attention for their diverse, challenging structural complexity and promising bioactivities. In the past decade, marine-derived microorganisms have become great repositories of novel tetramic acids. Here, we discuss the biological activities of 277 tetramic acids of eight classifications (simple 3-acyl tetramic acids, 3-oligoenoyltetramic acids, 3-decalinoyltetramic acid, 3-spirotetramic acids, macrocyclic tetramic acids, N-acylated tetramic acids, α-cyclopiazonic acid-type tetramic acids, and other tetramic acids) from marine-derived microbes, including fungi, actinobacteria, bacteria, and cyanobacteria, as reported in 195 research studies up to 2019.
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Capon RJ. Extracting value: mechanistic insights into the formation of natural product artifacts – case studies in marine natural products. Nat Prod Rep 2020; 37:55-79. [DOI: 10.1039/c9np00013e] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review highlights the importance of valuing natural product handling artifacts, to open a new window into, and provide a unique perspective of, bioactive chemical space.
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Affiliation(s)
- Robert J. Capon
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- St Lucia
- Australia
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25
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Costa JH, Wassano CI, Angolini CFF, Scherlach K, Hertweck C, Pacheco Fill T. Antifungal potential of secondary metabolites involved in the interaction between citrus pathogens. Sci Rep 2019; 9:18647. [PMID: 31819142 PMCID: PMC6901458 DOI: 10.1038/s41598-019-55204-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/23/2019] [Indexed: 12/27/2022] Open
Abstract
Numerous postharvest diseases have been reported that cause substantial losses of citrus fruits worldwide. Penicillium digitatum is responsible for up to 90% of production losses, and represent a problem for worldwide economy. In order to control phytopathogens, chemical fungicides have been extensively used. Yet, the use of some artificial fungicides cause concerns about environmental risks and fungal resistance. Therefore, studies focusing on new approaches, such as the use of natural products, are getting attention. Co-culture strategy can be applied to discover new bioactive compounds and to understand microbial ecology. Mass Spectrometry Imaging (MSI) was used to screen for potential antifungal metabolites involved in the interaction between Penicillium digitatum and Penicillium citrinum. MSI revealed a chemical warfare between the fungi: two tetrapeptides, deoxycitrinadin A, citrinadin A, chrysogenamide A and tryptoquialanines are produced in the fungi confrontation zone. Antimicrobial assays confirmed the antifungal activity of the investigated metabolites. Also, tryptoquialanines inhibited sporulation of P. citrinum. The fungal metabolites reported here were never described as antimicrobials until this date, demonstrating that co-cultures involving phytopathogens that compete for the same host is a positive strategy to discover new antifungal agents. However, the use of these natural products on the environment, as a safer strategy, needs further investigation. This paper aimed to contribute to the protection of agriculture, considering health and ecological risks.
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Affiliation(s)
- Jonas Henrique Costa
- Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil
| | | | | | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.,Chair of Natural Product Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Taícia Pacheco Fill
- Institute of Chemistry, University of Campinas, CP 6154, 13083-970, Campinas, SP, Brazil.
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Costa MS, Clark CM, Ómarsdóttir S, Sanchez LM, Murphy BT. Minimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac. JOURNAL OF NATURAL PRODUCTS 2019; 82:2167-2173. [PMID: 31335140 PMCID: PMC7197193 DOI: 10.1021/acs.jnatprod.9b00168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Libraries of microorganisms have been a cornerstone of drug discovery efforts since the mid-1950s, but strain duplication in some libraries has resulted in unwanted natural product redundancy. In the current study, we implemented a workflow that minimizes both the natural product overlap and the total number of bacterial isolates in a library. Using a collection expedition to Iceland as an example, we purified every distinct bacterial colony off isolation plates derived from 86 environmental samples. We employed our mass spectrometry (MS)-based IDBac workflow on these isolates to form groups of taxa based on protein MS fingerprints (3-15 kDa) and further distinguished taxa subgroups based on their degree of overlap within corresponding natural product spectra (0.2-2 kDa). This informed the decision to create a library of 301 isolates spanning 54 genera. This process required only 25 h of data acquisition and 2 h of analysis. In a separate experiment, we reduced the size of an existing library based on the degree of metabolic overlap observed in natural product MS spectra of bacterial colonies (from 833 to 233 isolates, a 72.0% size reduction). Overall, our pipeline allows for a significant reduction in costs associated with library generation and minimizes natural product redundancy entering into downstream biological screening efforts.
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Affiliation(s)
- Maria S Costa
- Faculty of Pharmaceutical Sciences , University of Iceland , Hagi, Hofsvallagata 53 , IS-107 Reykjavík , Iceland
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Illinois at Chicago , 833 South Wood Street (MC 781), Room 539 , Chicago , Illinois 60607 , United States
| | - Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Illinois at Chicago , 833 South Wood Street (MC 781), Room 539 , Chicago , Illinois 60607 , United States
| | - Sesselja Ómarsdóttir
- Faculty of Pharmaceutical Sciences , University of Iceland , Hagi, Hofsvallagata 53 , IS-107 Reykjavík , Iceland
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Illinois at Chicago , 833 South Wood Street (MC 781), Room 539 , Chicago , Illinois 60607 , United States
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Illinois at Chicago , 833 South Wood Street (MC 781), Room 539 , Chicago , Illinois 60607 , United States
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Offret C, Jégou C, Mounier J, Fleury Y, Le Chevalier P. New insights into the haemo- and coelo-microbiota with antimicrobial activities from Echinodermata and Mollusca. J Appl Microbiol 2019; 126:1023-1031. [PMID: 30586216 DOI: 10.1111/jam.14184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 11/26/2022]
Abstract
AIMS The aim of this study was to investigate the diversity of bacteria with antimicrobial activity present in the coelomic fluid and haemolymph of wild and healthy echinodermata and mollusca. METHODS AND RESULTS Collection expeditions of healthy marine molluscs and echinoderms were conducted in the Glenan archipelago in spring 2014. Members of the culturable microbiota present in the haemolymph, (haemo-microbiota) of Haliotis tuberculata (gastropoda, abalone) and Mytilus edulis (bivalvia, mussel), as well as in the coelomic fluid (coelo-microbiota) of Echinus esculentus (echinoidea, sea urchin) and Holothuria forskali (Holothuroidea, holothurian) were screened for antimicrobial activity, and further identified using 16S rRNA sequencing. Except for E. esculentus, culturable bacteria in the internal fluids of all studied organisms (mussel, abalone and holothurian) were more abundant than in seawater. The haemo- and coelo-microbiota with antimicrobial activity differed significantly between host species, in terms of abundance and diversity. Indeed, higher numbers were isolated from mussel than from abalone haemolymph. Moreover, in mussels and holothurians, bacteria with antimicrobial activities were predominantly Vibrio spp. (respectively 55 and 45%), while Pseudoalteromonas spp. were the most abundant (50%) in abalone haemolymph. Nevertheless, the activity spectra of these bacteria mainly included marine pathogens affiliated to the Vibrio genus. CONCLUSION The haemo- and coelo-microbiota with antimicrobial activities were significantly related to their host species and differed in terms of abundance and diversity. These bacteria may play a key role in host homeostasis against pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY This study brings new knowledge on the diversity of bacteria present in the internal fluids of two marine molluscs and two echinoderms and their antimicrobial activities towards marine pathogens.
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Affiliation(s)
- C Offret
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbiennes LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, Plouzané, France.,Food Sciences Department, Pavillon Paul-Comtois, Université Laval, Québec, Canada
| | - C Jégou
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
| | - J Mounier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbiennes LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, Plouzané, France
| | - Y Fleury
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
| | - P Le Chevalier
- Laboratoire de Biotechnologie et Chimie Marines LBCM EA3884, Université de Brest, Institut Universitaire Européen de la Mer, IUT Quimper, Quimper, France
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Wang JP, Shu Y, Liu SX, Hu JT, Sun CT, Zhou H, Gan D, Cai XY, Pu W, Cai L, Ding ZT. Expanstines A–D: four unusual isoprenoid epoxycyclohexenones generated byPenicillium expansumYJ-15 fermentation and photopromotion. Org Chem Front 2019. [DOI: 10.1039/c9qo01076a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Expanstines A–D fromP. expansumYJ-15 were derived under UV and visible light from 4′-oxomacrophoin A (5) and its acetate (6), which plausibly underwent a rare intramolecular photoene reaction and a [2 + 2] Paternò–Büchi photoaddition respectively.
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Raimundo I, Silva SG, Costa R, Keller-Costa T. Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth. Mar Drugs 2018; 16:E485. [PMID: 30518125 PMCID: PMC6316421 DOI: 10.3390/md16120485] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.
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Affiliation(s)
- Inês Raimundo
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Sandra G Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
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Atencio LA, Dal Grande F, Young GO, Gavilán R, Guzmán HM, Schmitt I, Mejía LC, Gutiérrez M. Antimicrobial-producing Pseudoalteromonas from the marine environment of Panama shows a high phylogenetic diversity and clonal structure. J Basic Microbiol 2018; 58:747-769. [PMID: 29938809 DOI: 10.1002/jobm.201800087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/11/2018] [Accepted: 06/02/2018] [Indexed: 01/01/2023]
Abstract
Pseudoalteromonas is a genus of marine bacteria often found in association with other organisms. Although several studies have examined Pseudoalteromonas diversity and their antimicrobial activity, its diversity in tropical environments is largely unexplored. We investigated the diversity of Pseudoalteromonas in marine environments of Panama using a multilocus phylogenetic approach. Furthermore we tested their antimicrobial capacity and evaluated the effect of recombination and mutation in shaping their phylogenetic relationships. The reconstruction of clonal relationships among 78 strains including 15 reference Pseudoalteromonas species revealed 43 clonal lineages, divided in pigmented and non-pigmented strains. In total, 39 strains displayed moderate to high activity against Gram-positive and Gram-negative bacteria and fungi. Linkage disequilibrium analyses showed that the Pseudoalteromonas strains of Panama have a highly clonal structure and that, although present, recombination is not frequent enough to break the association among alleles. This clonal structure is in contrast to the high rates of recombination generally reported for aquatic and marine bacteria. We propose that this structure is likely due to the symbiotic association with marine invertebrates of most strains analyzed. Our results also show that there are several putative new species of Pseudoalteromonas in Panama to be described.
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Affiliation(s)
- Librada A Atencio
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Republic of Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Giannina Ow Young
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Republic of Panama
| | - Ronnie Gavilán
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Republic of Panama.,National Center for Public Health, Instituto Nacional de Salud, Lima, Peru.,Environmental Management Department, Universidad San Ignacio de Loyola, Lima, Peru
| | - Héctor M Guzmán
- Smithsonian Tropical Research Institute, Ancon, Panama, Republic of Panama
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany.,Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe Universität Frankfurt, Frankfurt, Germany
| | - Luis C Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Republic of Panama.,Smithsonian Tropical Research Institute, Ancon, Panama, Republic of Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Republic of Panama
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Sarmiento-Vizcaíno A, Espadas J, Martín J, Braña AF, Reyes F, García LA, Blanco G. Atmospheric Precipitations, Hailstone and Rainwater, as a Novel Source of Streptomyces Producing Bioactive Natural Products. Front Microbiol 2018; 9:773. [PMID: 29740412 PMCID: PMC5924784 DOI: 10.3389/fmicb.2018.00773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/05/2018] [Indexed: 02/06/2023] Open
Abstract
A cultivation-dependent approach revealed that highly diverse populations of Streptomyces were present in atmospheric precipitations from a hailstorm event sampled in February 2016 in the Cantabrian Sea coast, North of Spain. A total of 29 bioactive Streptomyces strains isolated from small samples of hailstone and rainwater, collected from this hailstorm event, were studied here. Taxonomic identification by 16S rRNA sequencing revealed more than 20 different Streptomyces species, with their closest homologs displaying mainly oceanic but also terrestrial origins. Backward trajectory analysis revealed that the air-mass sources of the hailstorm event, with North Western winds, were originated in the Arctic Ocean (West Greenland and North Iceland) and Canada (Labrador), depending on the altitude. After traveling across the North Atlantic Ocean during 4 days the air mass reached Europe and precipitated as hailstone and rain water at the sampling place in Spain. The finding of Streptomyces species able to survive and disperse through the atmosphere increases our knowledge of the biogeography of genus Streptomyces on Earth, and reinforces our previous dispersion model, suggesting a generalized feature for the genus which could have been essential in his evolution. This unique atmospheric-derived Streptomyces collection was screened for production of bioactive secondary metabolites. Analyses of isolates ethyl acetate extracts by LC-UV-MS and further database comparison revealed an extraordinary diversity of bioactive natural products. One hundred molecules were identified, mostly displaying contrasted antibiotic and antitumor/cytotoxic activities, but also antiparasitic, antiviral, anti-inflammatory, neuroprotector, and insecticide properties. More interestingly, 38 molecules not identified in natural products databases might represent new natural products. Our results revealed for the first time an extraordinary diversity of Streptomyces species in the atmosphere able to produce an extraordinary repertoire of bioactive molecules, thus providing a very promising source for the discovery of novel pharmaceutical natural products.
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Affiliation(s)
- Aida Sarmiento-Vizcaíno
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Julia Espadas
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Luis A García
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Área de Ingeniería Química, Universidad de Oviedo, Oviedo, Spain
| | - Gloria Blanco
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
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Quezada M, Licona-Cassani C, Cruz-Morales P, Salim AA, Marcellin E, Capon RJ, Barona-Gómez F. Diverse Cone-Snail Species Harbor Closely Related Streptomyces Species with Conserved Chemical and Genetic Profiles, Including Polycyclic Tetramic Acid Macrolactams. Front Microbiol 2017; 8:2305. [PMID: 29225593 PMCID: PMC5705629 DOI: 10.3389/fmicb.2017.02305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 11/08/2017] [Indexed: 12/30/2022] Open
Abstract
Streptomyces are Gram-positive bacteria that occupy diverse ecological niches including host-associations with animals and plants. Members of this genus are known for their overwhelming repertoire of natural products, which has been exploited for almost a century as a source of medicines and agrochemicals. Notwithstanding intense scientific and commercial interest in Streptomyces natural products, surprisingly little is known of the intra- and/or inter-species ecological roles played by these metabolites. In this report we describe the chemical structures, biological properties, and biosynthetic relationships between natural products produced by Streptomyces isolated from internal tissues of predatory Conus snails, collected from the Great Barrier Reef, Australia. Using chromatographic, spectroscopic and bioassays methodology, we demonstrate that Streptomyces isolated from five different Conus species produce identical chemical and antifungal profiles - comprising a suite of polycyclic tetramic acid macrolactams (PTMs). To investigate possible ecological (and evolutionary) relationships we used genome analyses to reveal a close taxonomic relationship with other sponge-derived and free-living PTM producing Streptomyces (i.e., Streptomyces albus). In-depth phylogenomic analysis of PTM biosynthetic gene clusters indicated PTM structure diversity was governed by a small repertoire of genetic elements, including discrete gene acquisition events involving dehydrogenases. Overall, our study shows a Streptomyces-Conus ecological relationship that is concomitant with specific PTM chemical profiles. We provide an evolutionary framework to explain this relationship, driven by anti-fungal properties that protect Conus snails from fungal pathogens.
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Affiliation(s)
- Michelle Quezada
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Cuauhtemoc Licona-Cassani
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Angela A. Salim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
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Gleason FH, Gadd GM, Pitt JI, Larkum AWD. The roles of endolithic fungi in bioerosion and disease in marine ecosystems. II. Potential facultatively parasitic anamorphic ascomycetes can cause disease in corals and molluscs. Mycology 2017; 8:216-227. [PMID: 30123642 PMCID: PMC6059078 DOI: 10.1080/21501203.2017.1371802] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 10/29/2022] Open
Abstract
Anamorphic ascomycetes have been implicated as causative agents of diseases in tissues and skeletons of hard corals, in tissues of soft corals (sea fans) and in tissues and shells of molluscs. Opportunist marine fungal pathogens, such as Aspergillus sydowii, are important components of marine mycoplankton and are ubiquitous in the open oceans, intertidal zones and marine sediments. These fungi can cause infection in or at least can be associated with animals which live in these ecosystems. A. sydowii can produce toxins which inhibit photosynthesis in and the growth of coral zooxanthellae. The prevalence of many documented infections has increased in frequency and severity in recent decades with the changing impacts of physical and chemical factors, such as temperature, acidity and eutrophication. Changes in these factors are thought to cause significant loss of biodiversity in marine ecosystems on a global scale in general, and especially in coral reefs and shallow bays.
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Affiliation(s)
- Frank H. Gleason
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Geoffrey M. Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - John I. Pitt
- Food, Safety and Quality, CSIRO, Ryde, Australia
| | - Anthony W. D. Larkum
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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Zhang MM, Wong FT, Wang Y, Luo S, Lim YH, Heng E, Yeo WL, Cobb RE, Enghiad B, Ang EL, Zhao H. CRISPR-Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters. Nat Chem Biol 2017; 13:nchembio.2341. [PMID: 28398287 PMCID: PMC5634907 DOI: 10.1038/nchembio.2341] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/13/2017] [Indexed: 02/02/2023]
Abstract
Here we report an efficient CRISPR-Cas9 knock-in strategy to activate silent biosynthetic gene clusters (BGCs) in streptomycetes. We applied this one-step strategy to activate multiple BGCs of different classes in five Streptomyces species and triggered the production of unique metabolites, including a novel pentangular type II polyketide in Streptomyces viridochromogenes. This potentially scalable strategy complements existing activation approaches and facilitates discovery efforts to uncover new compounds with interesting bioactivities.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Biomedical Science Institutes, A*STAR, Singapore
| | - Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Shangwen Luo
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yee Hwee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences, A*STAR, Singapore
| | - Elena Heng
- Molecular Engineering Lab, Biomedical Science Institutes, A*STAR, Singapore
| | - Wan Lin Yeo
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Behnam Enghiad
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Yu HL, Jiang SH, Bu XL, Wang JH, Weng JY, Yang XM, He KY, Zhang ZG, Ao P, Xu J, Xu MJ. Structural diversity of anti-pancreatic cancer capsimycins identified in mangrove-derived Streptomyces xiamenensis 318 and post-modification via a novel cytochrome P450 monooxygenase. Sci Rep 2017; 7:40689. [PMID: 28098172 PMCID: PMC5241641 DOI: 10.1038/srep40689] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/08/2016] [Indexed: 01/12/2023] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) were identified as distinct secondary metabolites of the mangrove-derived Streptomyces xiamenensis 318. Together with three known compounds—ikarugamycin (1), capsimycin (2) and capsimycin B (3)—two new compounds, capsimycin C (4) with trans-diols and capsimycin D (5) with trans-configurations at C-13/C-14, have been identified. The absolute configurations of the tert/tert-diols moiety was determined in 4 by NMR spectroscopic analysis, CD spectral comparisons and semi-synthetic method. The post-modification mechanism of the carbocyclic ring at C-14/C-13 of compound 1 in the biosynthesis of an important intermediate 3 was investigated. A putative cytochrome P450 superfamily gene, SXIM_40690 (ikaD), which was proximally localized to the ikarugamycin biosynthetic pathway, was characterized. In vivo gene inactivation and complementation experiment confirmed that IkaD catalysed the epoxide-ring formation reaction and further hydroxylation of ethyl side chain to form capsimycin G (3′). Binding affinities and kinetic parameters for the interactions between ikarugamycin (1) and capsimycin B (3) with IkaD were measured with Surface Plasmon Resonance. The intermediate compound 3′ was isolated and identified as 30-hydroxyl-capsimycin B. The caspimycins 2 and 3, were transferred to methoxyl derivatives, 6 and 7, under acidic and heating conditions. Compounds 1–3 exhibited anti-proliferative activities against pancreatic carcinoma with IC50 values of 1.30–3.37 μM.
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Affiliation(s)
- He-Lin Yu
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu-Liang Bu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Institute of Oceanology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia-Hua Wang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Institute of Oceanology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing-Yi Weng
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kun-Yan He
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Ao
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Institute of Oceanology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Min-Juan Xu
- Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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Soler-Hurtado MM, Sandoval-Sierra JV, Machordom A, Diéguez-Uribeondo J. Aspergillus sydowii and Other Potential Fungal Pathogens in Gorgonian Octocorals of the Ecuadorian Pacific. PLoS One 2016; 11:e0165992. [PMID: 27902710 PMCID: PMC5130190 DOI: 10.1371/journal.pone.0165992] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/22/2016] [Indexed: 11/20/2022] Open
Abstract
Emerging fungal diseases are threatening ecosystems and have increased in recent decades. In corals, the prevalence and consequences of these infections have also increased in frequency and severity. Coral reefs are affected by an emerging fungal disease named aspergillosis, caused by Aspergillus sydowii. This disease and its pathogen have been reported along the Caribbean and Pacific coasts of Colombia. Despite this, an important number of coral reefs worldwide have not been investigated for the presence of this pathogen. In this work, we carried out the surveillance of the main coral reef of the Ecuadorian Pacific with a focus on the two most abundant and cosmopolitan species of this ecosystem, Leptogorgia sp. and Leptogorgia obscura. We collected 59 isolates and obtained the corresponding sequences of the Internal Transcribed Spacers (ITS) of the ribosomal DNA. These were phylogenetically analyzed using MrBayes, which indicated the presence of two isolates of the coral reef pathogen A. sydowii, as well as 16 additional species that are potentially pathogenic to corals. Although the analyzed gorgonian specimens appeared healthy, the presence of these pathogens, especially of A. sydowii, alert us to the potential risk to the health and future survival of the Pacific Ecuadorian coral ecosystem under the current scenario of increasing threats and stressors to coral reefs, such as habitat alterations by humans and global climate change.
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Affiliation(s)
- M. Mar Soler-Hurtado
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Departamento de Biodiversidad y Ecología de Invertebrados Marinos, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | | | - Annie Machordom
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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Offret C, Desriac F, Le Chevalier P, Mounier J, Jégou C, Fleury Y. Spotlight on Antimicrobial Metabolites from the Marine Bacteria Pseudoalteromonas: Chemodiversity and Ecological Significance. Mar Drugs 2016; 14:E129. [PMID: 27399731 PMCID: PMC4962019 DOI: 10.3390/md14070129] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/17/2022] Open
Abstract
This review is dedicated to the antimicrobial metabolite-producing Pseudoalteromonas strains. The genus Pseudoalteromonas hosts 41 species, among which 16 are antimicrobial metabolite producers. To date, a total of 69 antimicrobial compounds belonging to 18 different families have been documented. They are classified into alkaloids, polyketides, and peptides. Finally as Pseudoalteromonas strains are frequently associated with macroorganisms, we can discuss the ecological significance of antimicrobial Pseudoalteromonas as part of the resident microbiota.
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Affiliation(s)
- Clément Offret
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Florie Desriac
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Patrick Le Chevalier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Camille Jégou
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Yannick Fleury
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne LUBEM EA3882, Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
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Abstract
This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass spectrometry tools and workflows for revealing microbial chemistry. Analyst 2015; 140:4949-66. [PMID: 25996313 PMCID: PMC5444374 DOI: 10.1039/c5an00171d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.
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Pan M, Yuan D, Chen S, Xu A. Diversity and composition of the bacterial community in Amphioxus feces. J Basic Microbiol 2015; 55:1336-42. [PMID: 26173442 DOI: 10.1002/jobm.201500124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/23/2015] [Indexed: 12/12/2022]
Abstract
Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment.
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Affiliation(s)
- Minming Pan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Dongjuan Yuan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Shangwu Chen
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Anlong Xu
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Beijing University of Chinese Medicine, 11 Bei San Huan Dong Road, Chao-yang District, Beijing 100029, P. R. China
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Whalen KE, Poulson-Ellestad KL, Deering RW, Rowley DC, Mincer TJ. Enhancement of antibiotic activity against multidrug-resistant bacteria by the efflux pump inhibitor 3,4-dibromopyrrole-2,5-dione isolated from a Pseudoalteromonas sp. JOURNAL OF NATURAL PRODUCTS 2015; 78:402-412. [PMID: 25646964 DOI: 10.1021/np500775e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Members of the resistance nodulation cell division (RND) of efflux pumps play essential roles in multidrug resistance (MDR) in Gram-negative bacteria. Here, we describe the search for new small molecules from marine microbial extracts to block efflux and thus restore antibiotic susceptibility in MDR bacterial strains. We report the isolation of 3,4-dibromopyrrole-2,5-dione (1), an inhibitor of RND transporters, from Enterobacteriaceae and Pseudomonas aeruginosa, from the marine bacterium Pseudoalteromonas piscicida. 3,4-Dibromopyrrole-2,5-dione decreased the minimum inhibitory concentrations (MICs) of two fluoroquinolones, an aminoglycoside, a macrolide, a beta-lactam, tetracycline, and chloramphenicol between 2- and 16-fold in strains overexpressing three archetype RND transporters (AcrAB-TolC, MexAB-OprM, and MexXY-OprM). 3,4-Dibromopyrrole-2,5-dione also increased the intracellular accumulation of Hoechst 33342 in wild-type but not in transporter-deficient strains and prevented H33342 efflux (IC50 = 0.79 μg/mL or 3 μM), a hallmark of efflux pump inhibitor (EPI) functionality. A metabolomic survey of 36 Pseudoalteromonas isolates mapped the presence of primarily brominated metabolites only within the P. piscicida phylogenetic clade, where a majority of antibiotic activity was also observed, suggesting a link between halogenation and enhanced secondary metabolite biosynthetic potential. In sum, 3,4-dibromopyrrole-2,5-dione is a potent EPI and deserves further attention as an adjuvant to enhance the effectiveness of existing antibiotics.
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Affiliation(s)
| | | | - Robert W Deering
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - David C Rowley
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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