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Chukwudulue UM, Barger N, Dubovis M, Luzzatto Knaan T. Natural Products and Pharmacological Properties of Symbiotic Bacillota (Firmicutes) of Marine Macroalgae. Mar Drugs 2023; 21:569. [PMID: 37999393 PMCID: PMC10672036 DOI: 10.3390/md21110569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
The shift from the terrestrial to the marine environment to discover natural products has given rise to novel bioactive compounds, some of which have been approved for human medicine. However, the ocean, which makes up nearly three-quarters of the Earth's surface, contains macro- and microorganisms whose natural products are yet to be explored. Among these underexplored marine organisms are macroalgae and their symbiotic microbes, such as Bacillota, a phylum of mostly Gram-positive bacteria previously known as Firmicutes. Macroalgae-associated Bacillota often produce chemical compounds that protect them and their hosts from competitive and harmful rivals. Here, we summarised the natural products made by macroalgae-associated Bacillota and their pharmacological properties. We discovered that these Bacillota are efficient producers of novel biologically active molecules. However, only a few macroalgae had been investigated for chemical constituents of their Bacillota: nine brown, five red and one green algae. Thus, Bacillota, especially from the marine habitat, should be investigated for potential pharmaceutical leads. Moreover, additional diverse biological assays for the isolated molecules of macroalgae Bacillota should be implemented to expand their bioactivity profiles, as only antibacterial properties were tested for most compounds.
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Affiliation(s)
| | | | | | - Tal Luzzatto Knaan
- Department of Marine Biology, The Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa 103301, Israel; (U.M.C.); (N.B.); (M.D.)
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Dhakal D, Kokkaliari S, Rubin GM, Paul VJ, Ding Y, Luesch H. Biosynthesis of Lyngbyastatins 1 and 3, Cytotoxic Depsipeptides from an Okeania sp. Marine Cyanobacterium. J Nat Prod 2023; 86:85-93. [PMID: 36546857 PMCID: PMC10197921 DOI: 10.1021/acs.jnatprod.2c00782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lyngbyastatins (Lbns) 1 (1) and 3 (2) belong to a group of cyclic depsipeptides that inhibit cancer cell proliferation. These compounds have been isolated from different marine cyanobacterial collections, while further development of these compounds relies on their lengthy total synthesis. Biosynthetic studies of these compounds can provide viable strategies to access these compounds and develop new analogs. In this study, we report the identification and characterization of one Lbn biosynthetic gene cluster (BGC) from the marine cyanobacterium Okeania sp. VPG18-21. We initially identified 1 and 2 in the organic extract by mass spectrometry and performed the targeted isolation of these compounds, which feature a (2S,3R)-3-amino-2-methylpentanoic acid (MAP) and a (2S,3R)-3-amino-2-methylhexanoic acid (Amha) moiety, respectively. Parallel metagenomic sequencing of VPG18-21 led to the identification of a putative Lbn BGC that encodes six megaenzymes (LbnA-F), including one polyketide synthase (PKS, LbnE), four nonribosomal peptide synthetases (NRPSs, LbnB-D and -F), and one PKS-NRPS hybrid (LbnA). Bioinformatic analysis of these enzymes suggested that the BGC produces 1 and 2. Furthermore, our biochemical studies of three recombinant adenylation domains uncovered their substrate specificities, supporting the identity of the BGC. Finally, we identified near-complete Lbn-like BGCs in the genomes of two other marine cyanobacteria.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Sofia Kokkaliari
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Garret M. Rubin
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Valerie J. Paul
- Smithsonian Marine Station at Ft. Pierce, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
| | - Yousong Ding
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
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3
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Weiss MB, Médice RV, Jacinavicius FR, Pinto E, Crnkovic CM. Metabolomics Applied to Cyanobacterial Toxins and Natural Products. Adv Exp Med Biol 2023; 1439:21-49. [PMID: 37843804 DOI: 10.1007/978-3-031-41741-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The biological and chemical diversity of Cyanobacteria is remarkable. These ancient prokaryotes are widespread in nature and can be found in virtually every habitat on Earth where there is light and water. They are producers of an array of secondary metabolites with important ecological roles, toxic effects, and biotechnological applications. The investigation of cyanobacterial metabolites has benefited from advances in analytical tools and bioinformatics that are employed in metabolomic analyses. In this chapter, we review selected articles highlighting the use of targeted and untargeted metabolomics in the analyses of secondary metabolites produced by cyanobacteria. Here, cyanobacterial secondary metabolites have been didactically divided into toxins and natural products according to their relevance to toxicological studies and drug discovery, respectively. This review illustrates how metabolomics has improved the chemical analysis of cyanobacteria in terms of speed, sensitivity, selectivity, and/or coverage, allowing for broader and more complex scientific questions.
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Affiliation(s)
- Márcio Barczyszyn Weiss
- School of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo, Brazil
| | - Rhuana Valdetário Médice
- School of Pharmaceutical Sciences, Department of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, Brazil
| | - Fernanda Rios Jacinavicius
- School of Pharmaceutical Sciences, Department of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, Brazil
| | - Ernani Pinto
- Centre for Nuclear Energy in Agriculture, Division of Tropical Ecosystem Functioning, University of São Paulo, Piracicaba, Brazil
| | - Camila Manoel Crnkovic
- School of Pharmaceutical Sciences, Department of Biochemical and Pharmaceutical Technology, University of São Paulo, São Paulo, Brazil.
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Ricigliano VA, Cank KB, Todd DA, Knowles SL, Oberlies NH. Metabolomics-Guided Comparison of Pollen and Microalgae-Based Artificial Diets in Honey Bees. J Agric Food Chem 2022; 70:9790-9801. [PMID: 35881882 PMCID: PMC9372997 DOI: 10.1021/acs.jafc.2c02583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Managed honey bee colonies used for crop pollination are fed artificial diets to offset nutritional deficiencies related to land-use intensification and climate change. In this study, we formulated novel microalgae diets using Chlorella vulgaris and Arthrospira platensis (spirulina) biomass and fed them to young adult honey bee workers. Diet-induced changes in bee metabolite profiles were studied relative to a natural pollen diet using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) metabolomics. Untargeted analyses of pollen- and microalgae-fed bees revealed significant overlap, with 248 shared features determined by LC-MS and 87 shared features determined by GC-MS. Further metabolomic commonalities were evident upon subtraction of unique diet features. Twenty-five identified metabolites were influenced by diet, which included complex lipids, essential fatty acids, vitamins, and phytochemicals. The metabolomics results are useful to understand mechanisms underlying favorable growth performance as well as increased antioxidant and heat shock protein gene expression in bees fed the microalgae diets. We conclude that the tested microalgae have potential as sustainable feed additives and as a source of bee health-modulating natural products. Metabolomics-guided diet development could eventually help tailor feed interventions to achieve precision nutrition in honey bees and other livestock animals.
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Affiliation(s)
- Vincent A. Ricigliano
- Vincent
A. Ricigliano—Honey Bee Breeding, Genetics and Physiology Research, USDA-ARS, Baton
Rouge, Louisiana 70820, United States
| | - Kristof B. Cank
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402-6170, United States
| | - Daniel A. Todd
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402-6170, United States
| | - Sonja L. Knowles
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402-6170, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402-6170, United States
- .
Fax: (336) 334-5402
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5
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Abstract
BACKGROUND Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms. AIM OF REVIEW This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms. KEY SCIENTIFIC CONCEPTS OF REVIEW The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.
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Affiliation(s)
- Lina M Bayona
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, 2333 CR, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, 130-701, Seoul, Republic of Korea.
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Gueniche A, Perin O, Bouslimani A, Landemaine L, Misra N, Cupferman S, Aguilar L, Clavaud C, Chopra T, Khodr A. Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
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7
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Zhou Q, Hotta K, Deng Y, Yuan R, Quan S, Chen X. Advances in Biosynthesis of Natural Products from Marine Microorganisms. Microorganisms 2021; 9:2551. [PMID: 34946152 DOI: 10.3390/microorganisms9122551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/27/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023] Open
Abstract
Natural products play an important role in drug development, among which marine natural products are an underexplored resource. This review summarizes recent developments in marine natural product research, with an emphasis on compound discovery and production methods. Traditionally, novel compounds with useful biological activities have been identified through the chromatographic separation of crude extracts. New genome sequencing and bioinformatics technologies have enabled the identification of natural product biosynthetic gene clusters in marine microbes that are difficult to culture. Subsequently, heterologous expression and combinatorial biosynthesis have been used to produce natural products and their analogs. This review examines recent examples of such new strategies and technologies for the development of marine natural products.
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8
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Ding L, Bar-Shalom R, Aharonovich D, Kurisawa N, Patial G, Li S, He S, Yan X, Iwasaki A, Suenaga K, Zhu C, Luo H, Tian F, Fares F, Naman CB, Luzzatto-Knaan T. Metabolomic Characterization of a cf. Neolyngbya Cyanobacterium from the South China Sea Reveals Wenchangamide A, a Lipopeptide with In Vitro Apoptotic Potential in Colon Cancer Cells. Mar Drugs 2021; 19:md19070397. [PMID: 34356822 PMCID: PMC8307421 DOI: 10.3390/md19070397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolomics can be used to study complex mixtures of natural products, or secondary metabolites, for many different purposes. One productive application of metabolomics that has emerged in recent years is the guiding direction for isolating molecules with structural novelty through analysis of untargeted LC-MS/MS data. The metabolomics-driven investigation and bioassay-guided fractionation of a biomass assemblage from the South China Sea dominated by a marine filamentous cyanobacteria, cf. Neolyngbya sp., has led to the discovery of a natural product in this study, wenchangamide A (1). Wenchangamide A was found to concentration-dependently cause fast-onset apoptosis in HCT116 human colon cancer cells in vitro (24 h IC50 = 38 μM). Untargeted metabolomics, by way of MS/MS molecular networking, was used further to generate a structural proposal for a new natural product analogue of 1, here coined wenchangamide B, which was present in the organic extract and bioactive sub-fractions of the biomass examined. The wenchangamides are of interest for anticancer drug discovery, and the characterization of these molecules will facilitate the future discovery of related natural products and development of synthetic analogues.
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Affiliation(s)
- Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Rinat Bar-Shalom
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Naoaki Kurisawa
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
| | - Gaurav Patial
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shuang Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Xiaojun Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Arihiro Iwasaki
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Kiyotake Suenaga
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Chengcong Zhu
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Haixi Luo
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuli Tian
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuad Fares
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - C. Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
- Correspondence: (C.B.N.); (T.L.-K.)
| | - Tal Luzzatto-Knaan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
- Correspondence: (C.B.N.); (T.L.-K.)
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9
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Iwasaki A, Kurisawa N, Wang T, Li X, Luo H, Zhu C, Patial G, Yan X, He S, Luzzatto-Knaan T, Tian F, Naman CB, Suenaga K. Lingaoamide, a cyclic heptapeptide from a Chinese freshwater cyanobacterium Oscillatoria sp. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Hughes AH, Magot F, Tawfike AF, Rad-Menéndez C, Thomas N, Young LC, Stucchi L, Carettoni D, Stanley MS, Edrada-Ebel R, Duncan KR. Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics. Microorganisms 2021; 9:311. [PMID: 33546180 DOI: 10.3390/microorganisms9020311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 02/08/2023] Open
Abstract
With more than 156,000 described species, eukaryotic algae (both macro- and micro-algae) are a rich source of biological diversity, however their chemical diversity remains largely unexplored. Specialised metabolites with promising biological activities have been widely reported for seaweeds, and more recently extracts from microalgae have exhibited activity in anticancer, antimicrobial, and antioxidant screens. However, we are still missing critical information on the distinction of chemical profiles between macro- and microalgae, as well as the chemical space these metabolites cover. This study has used an untargeted comparative metabolomics approach to explore the chemical diversity of seven seaweeds and 36 microalgal strains. A total of 1390 liquid chromatography-mass spectrometry (LC-MS) features were detected, representing small organic algal metabolites, with no overlap between the seaweeds and microalgae. An in-depth analysis of four Dunaliella tertiolecta strains shows that environmental factors may play a larger role than phylogeny when classifying their metabolomic profiles.
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11
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Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs 2021; 19:20. [PMID: 33418911 DOI: 10.3390/md19010020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/31/2020] [Accepted: 01/02/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial natural products are important for the understanding of microbial interactions, chemical defense and communication, and have also served as an inspirational source for numerous pharmaceutical drugs. Tropical marine cyanobacteria have been highlighted as a great source of new natural products, however, few reports have appeared wherein a multi-omics approach has been used to study their natural products potential (i.e., reports are often focused on an individual natural product and its biosynthesis). This study focuses on describing the natural product genetic potential as well as the expressed natural product molecules in benthic tropical cyanobacteria. We collected from several sites around the world and sequenced the genomes of 24 tropical filamentous marine cyanobacteria. The informatics program antiSMASH was used to annotate the major classes of gene clusters. BiG-SCAPE phylum-wide analysis revealed the most promising strains for natural product discovery among these cyanobacteria. LCMS/MS-based metabolomics highlighted the most abundant molecules and molecular classes among 10 of these marine cyanobacterial samples. We observed that despite many genes encoding for peptidic natural products, peptides were not as abundant as lipids and lipopeptides in the chemical extracts. Our results highlight a number of highly interesting biosynthetic gene clusters for genome mining among these cyanobacterial samples.
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12
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Leber CA, Naman CB, Keller L, Almaliti J, Caro-Diaz EJE, Glukhov E, Joseph V, Sajeevan TP, Reyes AJ, Biggs JS, Li T, Yuan Y, He S, Yan X, Gerwick WH. Applying a Chemogeographic Strategy for Natural Product Discovery from the Marine Cyanobacterium Moorena bouillonii. Mar Drugs 2020; 18:E515. [PMID: 33066480 DOI: 10.3390/md18100515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
The tropical marine cyanobacterium Moorena bouillonii occupies a large geographic range across the Indian and Western Tropical Pacific Oceans and is a prolific producer of structurally unique and biologically active natural products. An ensemble of computational approaches, including the creation of the ORCA (Objective Relational Comparative Analysis) pipeline for flexible MS1 feature detection and multivariate analyses, were used to analyze various M. bouillonii samples. The observed chemogeographic patterns suggested the production of regionally specific natural products by M. bouillonii. Analyzing the drivers of these chemogeographic patterns allowed for the identification, targeted isolation, and structure elucidation of a regionally specific natural product, doscadenamide A (1). Analyses of MS2 fragmentation patterns further revealed this natural product to be part of an extensive family of herein annotated, proposed natural structural analogs (doscadenamides B–J, 2–10); the ensemble of structures reflect a combinatorial biosynthesis using nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) components. Compound 1 displayed synergistic in vitro cancer cell cytotoxicity when administered with lipopolysaccharide (LPS). These discoveries illustrate the utility in leveraging chemogeographic patterns for prioritizing natural product discovery efforts.
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13
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Sullivan P, Krunic A, Burdette JE, Orjala J. Laxaphycins B5 and B6 from the cultured cyanobacterium UIC 10484. J Antibiot (Tokyo) 2020; 73:526-33. [PMID: 32235860 DOI: 10.1038/s41429-020-0301-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/12/2020] [Accepted: 02/22/2020] [Indexed: 12/26/2022]
Abstract
Two laxaphycin type-B cyclic dodecapeptides, laxaphycins B5 and B6, were obtained from UIC 10484, a freshwater cf. Phormidium sp. Analysis using the 16S rRNA sequence found UIC 10484 to clade with UIC 10045, a known laxaphycin type-A and -B producer, and MS/MS analysis revealed the presence of two novel laxaphycin type-B compounds. The structures of the metabolites were elucidated using 2D NMR and MS/MS. The absolute configurations of the amino acids were determined by advanced Marfey's analysis. Both metabolites were evaluated against the same three cancer cell lines. The IC50 of both laxaphycins B5 and B6 was near 1 μM against breast cancer MDA-MB-231, melanoma MDA-MB-435, and ovarian cancer OVCAR3 cell lines.
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14
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Abstract
BACKGROUND Microalgae play a key role in ecosystems and are widely used in ecological status assessment. Research focusing on such organisms is then well developed and essential. Anyway, approaches for a better comprehension of their metabolome's response towards anthropogenic stressors are only emerging. AIM OF REVIEW This review presents the biochemical responses of various microalgae species towards several contaminants including metals and chemicals as pesticides or industrial compounds. We aim to provide a comprehensive and up-to-date overview of analytical approaches deciphering anthropogenic contaminants impact on microalgae metabolome dynamics, in order to bring out relevant biochemical markers that could be used for risk assessment. KEY SCIENTIFIC CONCEPTS OF REVIEW Studies to date on ecotoxicological metabolomics on microalgae are highly heterogeneous in both analytical techniques and resulting metabolite identification. There is a real need for studies using complementary approaches to determine biomarkers usable for ecological risk assessment.
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Affiliation(s)
- Léa Gauthier
- IRSTEA, UR EABX, 50 Avenue de Verdun, 33612, Cestas Cedex, France.
| | | | - Soizic Morin
- IRSTEA, UR EABX, 50 Avenue de Verdun, 33612, Cestas Cedex, France
| | - Nicolas Mazzella
- IRSTEA, UR EABX, 50 Avenue de Verdun, 33612, Cestas Cedex, France
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15
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Sogin EM, Puskás E, Dubilier N, Liebeke M. Marine Metabolomics: a Method for Nontargeted Measurement of Metabolites in Seawater by Gas Chromatography-Mass Spectrometry. mSystems 2019; 4:e00638-19. [PMID: 31822601 DOI: 10.1128/mSystems.00638-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats. Microbial communities exchange molecules with their environment, which plays a major role in regulating global biogeochemical cycles and climate. While extracellular metabolites are commonly measured in terrestrial and limnic ecosystems, the presence of salt in marine habitats limits the nontargeted analyses of the ocean exometabolome using mass spectrometry (MS). Current methods require salt removal prior to sample measurements, which can alter the molecular composition of the metabolome and limit the types of compounds detected by MS. To overcome these limitations, we developed a gas chromatography MS (GC-MS) method that avoids sample altering during salt removal and that detects metabolites down to nanomolar concentrations from less than 1 ml of seawater. We applied our method (SeaMet) to explore marine metabolomes in vitro and in vivo. First, we measured the production and consumption of metabolites during the culture of a heterotrophic bacterium, Marinobacter adhaerens. Our approach revealed successional uptake of amino acids, while sugars were not consumed. These results show that exocellular metabolomics provides insights into nutrient uptake and energy conservation in marine microorganisms. We also applied SeaMet to explore the in situ metabolome of coral reef and mangrove sediment porewaters. Despite the fact that these ecosystems occur in nutrient-poor waters, we uncovered high concentrations of sugars and fatty acids, compounds predicted to play a key role for the abundant and diverse microbial communities in coral reef and mangrove sediments. Our data demonstrate that SeaMet advances marine metabolomics by enabling a nontargeted and quantitative analysis of marine metabolites, thus providing new insights into nutrient cycles in the oceans. IMPORTANCE Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolomics, we developed SeaMet, which overcomes the limitations of salt on metabolite detection. Considering that the oceans contain the largest dissolved organic matter pool on Earth, describing the marine metabolome using nontargeted approaches is critical for understanding the drivers behind element cycles, biotic interactions, ecosystem function, and atmospheric CO2 storage. Our method complements both targeted marine metabolomic investigations as well as other “omics” (e.g., genomics, transcriptomics, and proteomics) approaches by providing an avenue for studying the chemical interaction between marine microbes and their habitats.
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Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst 2019; 9:600-608.e4. [PMID: 31629686 DOI: 10.1016/j.cels.2019.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.
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Affiliation(s)
- Liu Cao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Kelsey L Alexander
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Tiago Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Robby Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Rodolfo A S Benitez
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA
| | - Luke R Thompson
- Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, MS, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Md-Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - James T Morton
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Department of Mathematics and Mechanics, St. Petersburg State University, St. Petersburg, Russia
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; Interdepartmental program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego School of Medicine, San Diego, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, San Diego, CA, USA
| | - Hosein Mohimani
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, USA.
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Kim Tiam S, Gugger M, Demay J, Le Manach S, Duval C, Bernard C, Marie B. Insights into the Diversity of Secondary Metabolites of Planktothrix Using a Biphasic Approach Combining Global Genomics and Metabolomics. Toxins (Basel) 2019; 11:E498. [PMID: 31461939 PMCID: PMC6784222 DOI: 10.3390/toxins11090498] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with diverse chemical structures and potent biological activities and toxicities. The chemical identification of these compounds remains a major bottleneck. Strategies that can prioritize the most prolific strains and novel compounds are of great interest. Here, we combine chemical analysis and genomics to investigate the chemodiversity of secondary metabolites based on their pattern of distribution within some cyanobacteria. Planktothrix being a cyanobacterial genus known to form blooms worldwide and to produce a broad spectrum of toxins and other bioactive compounds, we applied this combined approach on four closely related strains of Planktothrix. The chemical diversity of the metabolites produced by the four strains was evaluated using an untargeted metabolomics strategy with high-resolution LC-MS. Metabolite profiles were correlated with the potential of metabolite production identified by genomics for the different strains. Although, the Planktothrix strains present a global similarity in terms of a biosynthetic cluster gene for microcystin, aeruginosin, and prenylagaramide for example, we found remarkable strain-specific chemodiversity. Only few of the chemical features were common to the four studied strains. Additionally, the MS/MS data were analyzed using Global Natural Products Social Molecular Networking (GNPS) to identify molecular families of the same biosynthetic origin. In conclusion, we depict an efficient, integrative strategy for elucidating the chemical diversity of a given genus and link the data obtained from analytical chemistry to biosynthetic genes of cyanobacteria.
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Affiliation(s)
- Sandra Kim Tiam
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 05, France
| | - Justine Demay
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Séverine Le Manach
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Charlotte Duval
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France
| | - Benjamin Marie
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS, MNHN Molécules de Communication et Adaptation des Micro-organismes (MCAM), équipe "Cyanobactéries, Cyanotoxines et Environnement", 12 rue Buffon - RDC bâtiment de cryptogamie - CP 39, 75231 Paris Cedex 05, France.
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18
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Barbosa AJM, Roque ACA. Free Marine Natural Products Databases for Biotechnology and Bioengineering. Biotechnol J 2019; 14:e1800607. [PMID: 31297982 DOI: 10.1002/biot.201800607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/14/2019] [Indexed: 12/16/2022]
Abstract
Marine organisms and micro-organisms are a source of natural compounds with unique chemical features. These chemical properties are useful for the discovery of new functions and applications of marine natural products (MNPs). To extensively exploit the potential implementations of MNPs, they are gathered in chemical databases that allow their study and screening for applications of biotechnological interest. However, the classification of MNPs is currently poor in generic chemical databases. The present availability of free-access-focused MNP databases is scarce and the molecular diversity of these databases is still very low when compared to the paid-access ones. In this review paper, the current scenario of free-access MNP databases is presented as well as the hindrances involved in their development, mainly compound dereplication. Examples and opportunities for using freely accessible MNP databases in several important areas of biotechnology are also assessed. The scope of this paper is, as well, to notify the latent potential of these information sources for the discovery and development of new MNPs in biotechnology, and push future efforts to develop a public domain MNP database freely available for the scientific community.
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Affiliation(s)
- Arménio J M Barbosa
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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19
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Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biol 2019; 17:47. [PMID: 31189482 PMCID: PMC6560912 DOI: 10.1186/s12915-019-0660-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects on molecular and microbial diversity of the skin are unknown. We evaluated the impact of four beauty products (a facial lotion, a moisturizer, a foot powder, and a deodorant) on 11 volunteers over 9 weeks. RESULTS Mass spectrometry and 16S rRNA inventories of the skin revealed decreases in chemical as well as in bacterial and archaeal diversity on halting deodorant use. Specific compounds from beauty products used before the study remain detectable with half-lives of 0.5-1.9 weeks. The deodorant and foot powder increased molecular, bacterial, and archaeal diversity, while arm and face lotions had little effect on bacterial and archaeal but increased chemical diversity. Personal care product effects last for weeks and produce highly individualized responses, including alterations in steroid and pheromone levels and in bacterial and archaeal ecosystem structure and dynamics. CONCLUSIONS These findings may lead to next-generation precision beauty products and therapies for skin disorders.
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Affiliation(s)
- Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Department for Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Chris Callewaert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Center for Microbial Ecology and Technology, Ghent University, 9000, Ghent, Belgium
| | - Amnon Amir
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Ji-Nu Kim
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Tara Schwartz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Caitriona Brennan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92037, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, 92307, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92037, USA.
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Fasciotti M, Souza GHMF, Astarita G, Costa ICR, Monteiro TVC, Teixeira CMLL, Eberlin MN, Sarpal AS. Investigating the Potential of Ion Mobility-Mass Spectrometry for Microalgae Biomass Characterization. Anal Chem 2019; 91:9266-9276. [DOI: 10.1021/acs.analchem.9b02172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maíra Fasciotti
- National Institute of Metrology, Quality and Technology (INMETRO), Division of Chemical and Thermal Metrology, Laboratory of Organic Analysis, 25250-020, Duque de Caxias, Rio de Janeiro, Brazil
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas − UNICAMP, 13083-970 Campinas, São Paulo, Brazil
| | - Gustavo H. M. F. Souza
- MS Applications and Development Laboratory, Waters Corporation, 06455-000 Barueri, São Paulo, Brazil
| | - Giuseppe Astarita
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington DC 20007, United States
| | - Ingrid C. R. Costa
- National Institute of Metrology, Quality and Technology (INMETRO), Division of Chemical and Thermal Metrology, Laboratory of Organic Analysis, 25250-020, Duque de Caxias, Rio de Janeiro, Brazil
| | - Thays. V. C. Monteiro
- National Institute of Metrology, Quality and Technology (INMETRO), Division of Chemical and Thermal Metrology, Laboratory of Organic Analysis, 25250-020, Duque de Caxias, Rio de Janeiro, Brazil
| | - Claudia M. L. L. Teixeira
- Microalgal Biotechnology Laboratory, National Institute of Technology (INT), 20081-312 Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos N. Eberlin
- Mackenzie Presbyterian University, School of Engineering, 01302-907 São Paulo, São Paulo, Brazil
| | - Amarijt S. Sarpal
- National Institute of Metrology, Quality and Technology (INMETRO), Division of Chemical and Thermal Metrology, Laboratory of Organic Analysis, 25250-020, Duque de Caxias, Rio de Janeiro, Brazil
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Fox Ramos AE, Evanno L, Poupon E, Champy P, Beniddir MA. Natural products targeting strategies involving molecular networking: different manners, one goal. Nat Prod Rep 2019; 36:960-980. [PMID: 31140509 DOI: 10.1039/c9np00006b] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to 2019Landmark advances in bioinformatics tools have recently enhanced the field of natural products research, putting today's natural product chemists in the enviable position of being able to perform the efficient targeting/discovery of previously undescribed molecules by expediting the prioritization of the isolation workflow. Among these advances, MS/MS molecular networking has appeared as a promising approach to dereplicate complex natural product mixtures, leading to a real revolution in the "art of natural product isolation" by accelerating the pace of research of this field. This review illustrates through selected cornerstone studies the new thinking in natural product isolation by drawing a parallel between the different underlying philosophies behind the use of molecular networking in targeting natural products.
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Affiliation(s)
- Alexander E Fox Ramos
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Laurent Evanno
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Erwan Poupon
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Pierre Champy
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles", BioCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
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Freitas S, Silva NG, Sousa ML, Ribeiro T, Rosa F, Leão PN, Vasconcelos V, Reis MA, Urbatzka R. Chlorophyll Derivatives from Marine Cyanobacteria with Lipid-Reducing Activities. Mar Drugs 2019; 17:md17040229. [PMID: 30999602 PMCID: PMC6520785 DOI: 10.3390/md17040229] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/11/2019] [Accepted: 04/14/2019] [Indexed: 12/12/2022] Open
Abstract
Marine organisms, particularly cyanobacteria, are important resources for the production of bioactive secondary metabolites for the treatment of human diseases. In this study, a bioassay-guided approach was used to discover metabolites with lipid-reducing activity. Two chlorophyll derivatives were successfully isolated, the previously described 132-hydroxy-pheophytin a (1) and the new compound 132-hydroxy-pheofarnesin a (2). The structure elucidation of the new compound 2 was established based on one- and two-dimensional (1D and 2D) NMR spectroscopy and mass spectrometry. Compounds 1 and 2 showed significant neutral lipid-reducing activity in the zebrafish Nile red fat metabolism assay after 48 h of exposure with a half maximal effective concentration (EC50) of 8.9 ± 0.4 µM for 1 and 15.5 ± 1.3 µM for 2. Both compounds additionally reduced neutral lipid accumulation in 3T3-L1 multicellular spheroids of murine preadipocytes. Molecular profiling of mRNA expression of some target genes was evaluated for the higher potent compound 1, which indicated altered peroxisome proliferator activated receptor gamma (PPARγ) mRNA expression. Lipolysis was not affected. Different food materials (Spirulina, Chlorella, spinach, and cabbage) were evaluated for the presence of 1, and the cyanobacterium Spirulina, with GRAS (generally regarded as safe) status for human consumption, contained high amounts of 1. In summary, known and novel chlorophyll derivatives were discovered from marine cyanobacteria with relevant lipid-reducing activities, which in the future may be developed into nutraceuticals.
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Affiliation(s)
- Sara Freitas
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
- FCUP, Faculty of Science, Department of Biology, University of Porto, Rua do Campo, Alegre, 4169-007 Porto, Portugal.
| | - Natália Gonçalves Silva
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Maria Lígia Sousa
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Tiago Ribeiro
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Filipa Rosa
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Pedro N Leão
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Vitor Vasconcelos
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
- FCUP, Faculty of Science, Department of Biology, University of Porto, Rua do Campo, Alegre, 4169-007 Porto, Portugal.
| | - Mariana Alves Reis
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Ralph Urbatzka
- Interdisciplinary Center of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
- FCUP, Faculty of Science, Department of Biology, University of Porto, Rua do Campo, Alegre, 4169-007 Porto, Portugal.
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23
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Abstract
Microbes use metabolic exchange to sense and respond to their changing environment. Surfactins, produced by Bacillus subtilis, have been extensively studied for their role in biofilm formation, biosurfactant properties, and antimicrobial activity, affecting the surrounding microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis, originally isolated with B. subtilis, is not antagonized by the presence of surfactins and is actually attracted to them. We demonstrate here for the first time that P. dendritiformis is also actively degrading surfactins produced by B. subtilis and accumulating the degradation products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a deterrent highlight the diverse role natural products have in shaping the environment and establishing mixed communities.
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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, United States
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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24
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Davison JR, Bewley CA. Antimicrobial Chrysophaentin Analogs Identified from Laboratory Cultures of the Marine Microalga Chrysophaeum taylorii. J Nat Prod 2019; 82:148-153. [PMID: 30623657 PMCID: PMC8414558 DOI: 10.1021/acs.jnatprod.8b00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A laboratory culture of the colonial marine alga Chrysophaeum taylorii NIES-1699 yielded a set of new bioactive chrysophaentin analogs, and their structures were determined by HRESIMS and NMR spectroscopy. Differences in the metabolites identified between cultured C. taylorii NIES-1699 and field-collected strains from the U.S. Virgin Islands revealed additional structure-activity relationships for the Gram-positive antibiotic activity of the chrysophaentins. The presence of new hemichrysophaentins and a C-C linked biphenyl analog suggest novel features of their biosynthetic pathway. Bayesian analysis of the alignment of the 18S rRNA gene places the microalga C. taylorii in the pelagophyte clade.
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Affiliation(s)
- Jack R. Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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25
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Wolfender JL, Nuzillard JM, van der Hooft JJJ, Renault JH, Bertrand S. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Anal Chem 2018; 91:704-742. [DOI: 10.1021/acs.analchem.8b05112] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jean-Marc Nuzillard
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | | | - Jean-Hugues Renault
- Institut de Chimie Moléculaire de Reims, UMR CNRS 7312, Université de Reims Champagne Ardenne, 51687 Reims Cedex 2, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 44035 Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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26
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Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. Dereplication of microbial metabolites through database search of mass spectra. Nat Commun 2018; 9:4035. [PMID: 30279420 PMCID: PMC6168521 DOI: 10.1038/s41467-018-06082-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022] Open
Abstract
Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.
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Affiliation(s)
- Hosein Mohimani
- Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia
| | - Liu Cao
- Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Egor Shcherbin
- National Research University Higher School of Economics, St. Petersburg, Russia
| | - Louis-Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Pharmacology and Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
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27
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Kang KB, Park EJ, da Silva RR, Kim HW, Dorrestein PC, Sung SH. Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication. J Nat Prod 2018; 81:1819-1828. [PMID: 30106290 DOI: 10.1021/acs.jnatprod.8b00292] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The integration of LC-MS/MS molecular networking and in silico MS/MS fragmentation is an emerging method for dereplication of natural products. In the present study, a targeted isolation of natural products using a new in silico-based annotation tool named Network Annotation Propagation (NAP) is described. NAP improves accuracy of in silico fragmentation analyses by reranking candidate structures based on the network topology from MS/MS-based molecular networking. Annotation for the MS/MS spectral network of the Sageratia theezans twig extract was performed using NAP, and most molecular families within the network, including the known triterpenoids 1-7, could be putatively annotated, without relying on any previous reports of molecules from this species. Based on the in silico dereplication results, molecules were prioritized for isolation. In total, six dicoumaroyl 8- O-4' neolignans (8-13) and three dicoumaroyl lignans (14-16) were isolated from the twigs of S. theezans and structurally characterized by spectroscopic analyses. Isolates were evaluated for their neuroprotective activity, and compounds 14-16 showed potent protective effects against glutamate-induced oxidative stress in mouse HT22 cells at a concentration of 12.5 μM.
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Affiliation(s)
- Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Eun Jin Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Hyun Woo Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences , Seoul National University , Seoul 08826 , Republic of Korea
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28
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Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA. Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol 2018; 3:319-27. [PMID: 29358742 DOI: 10.1038/s41564-017-0094-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/08/2017] [Indexed: 11/09/2022]
Abstract
Peptidic natural products (PNPs) include many antibiotics and other bioactive compounds. While the recent launch of the Global Natural Products Social (GNPS) molecular networking infrastructure is transforming PNP discovery into a high-throughput technology, PNP identification algorithms are needed to realize the potential of the GNPS project. GNPS relies on the assumption that each connected component of a molecular network (representing related metabolites) illuminates the 'dark matter of metabolomics' as long as it contains a known metabolite present in a database. We reveal a surprising diversity of PNPs produced by related bacteria and show that, contrary to the 'comparative metabolomics' assumption, two related bacteria are unlikely to produce identical PNPs (even though they are likely to produce similar PNPs). Since this observation undermines the utility of GNPS, we developed a PNP identification tool, VarQuest, that illuminates the connected components in a molecular network even if they do not contain known PNPs and only contain their variants. VarQuest reveals an order of magnitude more PNP variants than all previous PNP discovery efforts and demonstrates that GNPS already contains spectra from 41% of the currently known PNP families. The enormous diversity of PNPs suggests that biosynthetic gene clusters in various microorganisms constantly evolve to generate a unique spectrum of PNP variants that differ from PNPs in other species.
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