Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium.

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Author response: Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

10.7554/elife.24214.027 ◽

2017 ◽

Author(s):

Tal Luzzatto-Knaan ◽

Neha Garg ◽

Mingxun Wang ◽

Evgenia Glukhov ◽

Yao Peng ◽

...

Keyword(s):

Mass Spectrometry ◽

Chemical Diversity ◽

Mass Spectrometry Data ◽

Author Response ◽

Marine Cyanobacteria ◽

Cyanobacteria And Algae

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Decision letter: Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae

10.7554/elife.24214.026 ◽

2017 ◽

Keyword(s):

Mass Spectrometry ◽

Chemical Diversity ◽

Mass Spectrometry Data ◽

Marine Cyanobacteria ◽

Cyanobacteria And Algae

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Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics

Microorganisms ◽

10.3390/microorganisms9020311 ◽

2021 ◽

Vol 9 (2) ◽

pp. 311

Author(s):

Alison H. Hughes ◽

Florent Magot ◽

Ahmed F. Tawfike ◽

Cecilia Rad-Menéndez ◽

Naomi Thomas ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Biological Diversity ◽

Chemical Space ◽

Biological Activities ◽

Chemical Diversity ◽

Liquid Chromatography Mass Spectrometry ◽

Depth Analysis ◽

Comparative Metabolomics ◽

Chemical Profiles

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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Screening Mold Colonies by Using Two Toxicity Assays Revealed Indoor Strains of Aspergillus calidoustus Producing Ophiobolins G and K

Toxins ◽

10.3390/toxins11120683 ◽

2019 ◽

Vol 11 (12) ◽

pp. 683 ◽

Cited By ~ 2

Author(s):

Marja Johanna Salo ◽

Tamás Marik ◽

Ottó Bencsik ◽

Raimo Mikkola ◽

László Kredics ◽

...

Keyword(s):

Mass Spectrometry ◽

Cell Proliferation ◽

Sperm Motility ◽

High Performance ◽

Biological Activities ◽

Membrane Integrity ◽

Opportunistic Pathogen ◽

Mass Spectrometry Data ◽

Toxic Substances ◽

Boar Sperm

The occurrence and toxin production of the opportunistic pathogen Aspergillus calidoustus in Finnish buildings is not well documented in the literature. We tracked and identified four A. calidoustus colonies cultivated from indoor settled dusts and revealed the biological activities of crude biomass extracts. The toxic substances were identified as 6-epi-ophiobolin K, ophiobolin K, and ophiobolin G by high-performance liquid chromatography–mass spectrometry (HPLC-MS) based on chromatographic and mass spectrometry data (MS and MS/MS) on the crude extract of A. calidoustus strain MH34. A total of 29 fungal colonies collected from settled dust in an office room reported for indoor-air-related illnesses were screened for toxins that inhibited boar sperm motility in the BSMI (boar sperm motility inhibiting) assay and cell proliferation in the ICP (inhibition of cell proliferation) assays with PK-15 cells. Out of the 27 colonies tested as toxic, 12 colonies exhibiting conidiophores representative of the genera Chaetomium, Penicillium, and Paecilomyces were excluded from the study, while 13 colonies exhibited Aspergillus-like conidiophores. Biomass suspensions of these colonies were divided into two categories: Category 1 colonies (n = 4), toxic in the BSMI assay and the ICP assays, emitted blue fluorescence and grew at 37 °C; Category 2 colonies (n = 9), only toxic in the ICP assay, emitted orange fluorescence and exhibited limited or no growth at 37 °C. Colonies in Category 1 were pure-cultured, and the strains were named as MH4, MH21, MH34, MH36. Strain MH34 was identified as A. calidoustus by the internal transcribed spacer (ITS) sequences. Ethanol-soluble dry substances extracted from the biomass of the pure cultures exhibited a toxicological profile in the BSMI assay, SMID (sperm membrane integrity damage) assay, and ICP assay similar to that exhibited by pure ophiobolin A. Overall, the viable conidia of A. calidoustus in indoor settled dusts deserve attention when potentially hazardous mold species are monitored.

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Lessons from Exploring Chemical Space and Chemical Diversity of Propolis Components

International Journal of Molecular Sciences ◽

10.3390/ijms21144988 ◽

2020 ◽

Vol 21 (14) ◽

pp. 4988 ◽

Cited By ~ 1

Author(s):

Trong D. Tran ◽

Steven M. Ogbourne ◽

Peter R. Brooks ◽

Norberto Sánchez-Cruz ◽

José L. Medina-Franco ◽

...

Keyword(s):

Honey Bee ◽

Broad Spectrum ◽

Chemical Space ◽

Biological Activities ◽

Stingless Bee ◽

Chemical Diversity ◽

Commercial Interest ◽

Compound Database ◽

Ancient Times ◽

Unique Compound

Propolis is a natural resinous material produced by bees and has been used in folk medicines since ancient times. Due to it possessing a broad spectrum of biological activities, it has gained significant scientific and commercial interest over the last two decades. As a result of searching 122 publications reported up to the end of 2019, we assembled a unique compound database consisting of 578 components isolated from both honey bee propolis and stingless bee propolis, and analyzed the chemical space and chemical diversity of these compounds. The results demonstrated that both honey bee propolis and stingless bee propolis are valuable sources for pharmaceutical and nutraceutical development.

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A robotic prebiotic chemist probes long term reactions of complexifying mixtures

Nature Communications ◽

10.1038/s41467-021-23828-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Silke Asche ◽

Geoffrey J. T. Cooper ◽

Graham Keenan ◽

Cole Mathis ◽

Leroy Cronin

Keyword(s):

Mass Spectrometry ◽

Multicomponent Reactions ◽

Prebiotic Chemistry ◽

Chemical Space ◽

Mass Spectrometry Data ◽

Living Systems ◽

High Complexity ◽

Long Term Experiments ◽

Emergence Of Life

AbstractTo experimentally test hypotheses about the emergence of living systems from abiotic chemistry, researchers need to be able to run intelligent, automated, and long-term experiments to explore chemical space. Here we report a robotic prebiotic chemist equipped with an automatic sensor system designed for long-term chemical experiments exploring unconstrained multicomponent reactions, which can run autonomously over long periods. The system collects mass spectrometry data from over 10 experiments, with 60 to 150 algorithmically controlled cycles per experiment, running continuously for over 4 weeks. We show that the robot can discover the production of high complexity molecules from simple precursors, as well as deal with the vast amount of data produced by a recursive and unconstrained experiment. This approach represents what we believe to be a necessary step towards the design of new types of Origin of Life experiments that allow testable hypotheses for the emergence of life from prebiotic chemistry.

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Mining Public Mass Spectrometry Data to Characterize the Diversity and Ubiquity of P. aeruginosa Specialized Metabolites

Metabolites ◽

10.3390/metabo10110445 ◽

2020 ◽

Vol 10 (11) ◽

pp. 445

Author(s):

Andrew C. Lybbert ◽

Justin L. Williams ◽

Ruma Raghuvanshi ◽

A. Daniel Jones ◽

Robert A. Quinn

Keyword(s):

Mass Spectrometry ◽

Pathogenic Bacteria ◽

Acyl Chain ◽

Chemical Diversity ◽

Mass Spectrometry Data ◽

Clinical Samples ◽

Tandem Mass ◽

Human Teeth ◽

Specialized Metabolites ◽

Public Data

Pseudomonas aeruginosa is a ubiquitous environmental bacterium that causes chronic infections of burn wounds and in the lungs of cystic fibrosis (CF) patients. Vital to its infection is a myriad of specialized metabolites that serve a variety of biological roles including quorum sensing, metal chelation and inhibition of other competing bacteria. This study employed newly available algorithms for searching individual tandem mass (MS/MS) spectra against the publicly available Global Natural Product Social Molecular Networking (GNPS) database to identify the chemical diversity of these compounds and their presence in environmental, laboratory and clinical samples. For initial characterization, the metabolomes of eight clinical isolates of P. aeruginosa were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and uploaded to GNPS for spectral searching. Quinolones, rhamnolipids, phenazines and siderophores were identified and characterized; including the discovery of modified forms of the iron chelator pyochelin. Quinolones were highly diverse with the three base forms Pseudomonas quinolone signal 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), 4-heptyl-4(1H)-quinolone (HHQ) and 2-heptyl-4-quinolone-N-oxide (HQNO) having extensive variation in the length of their acyl chain from as small as 3 carbons to as large as 17. Rhamnolipids were limited to either one or two sugars with a limited set of fatty acyl chains, but the base lipid form without the rhamnose was also detected. These specialized metabolites were identified from diverse sources including ant-fungal mutualist dens, soil, plants, human teeth, feces, various lung mucus samples and cultured laboratory isolates. Their prevalence in fecal samples was particularly notable as P. aeruginosa is not known as a common colonizer of the human gut. The chemical diversity of the compounds identified, particularly the quinolones, demonstrates a broad spectrum of chemical properties within these the metabolite groups with likely significant impacts on their biological functions. Mining public data with GNPS enables a new approach to characterize the chemical diversity of biological organisms, which includes enabling the discovery of new chemistry from pathogenic bacteria.

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Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Entropy ◽

10.3390/e15104066 ◽

2013 ◽

Vol 15 (12) ◽

pp. 4066-4083 ◽

Cited By ~ 17

Author(s):

Jakob Andersen ◽

Tommy Andersen ◽

Christoph Flamm ◽

Martin Hanczyc ◽

Daniel Merkle ◽

...

Keyword(s):

Mass Spectrometry ◽

Chemical Space ◽

Mass Spectrometry Data ◽

Graph Grammars

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Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.12.120 ◽

2016 ◽

Vol 12 ◽

pp. 1250-1268 ◽

Cited By ~ 28

Author(s):

Andrew W Truman

Keyword(s):

Amino Acids ◽

Chemical Reactions ◽

Chemical Space ◽

Biological Activities ◽

Chemical Diversity ◽

Future Prospects ◽

Signalling Molecules ◽

Modified Peptides ◽

Pathway Discovery ◽

Anti Hiv

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.

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