using-open-source-maldi-tof-ms-idbac-pipeline-for-analysis-microbial

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, ...

University of Illinois at Chicago

University of Iceland

The oceans remain a major source of natural compounds with potential in pharmacology. In particular, during the last few decades, marine cyanobacteria have been in focus as producers of interesting bioactive compounds, especially for the treatment of cancer. In this study, the anticancer potential of extracts from twenty eight marine cyanobacteria strains, belonging to the underexplored picoplanktonic genera, Cyanobium, Synechocystis and Synechococcus, and the filamentous genera, Nodosilinea, Leptolyngbya, Pseudanabaena and Romeria, were assessed in eight human tumor cell lines. First, a crude extract was obtained by dichloromethane:methanol extraction, and from it, three fractions were separated in a Si column chromatography. The crude extract and fractions were tested in eight human cancer cell lines for cell viability/toxicity, accessed with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and lactic dehydrogenase release (LDH) assays. Eight point nine percent of the strains revealed strong cytotoxicity; 17.8% showed moderate cytotoxicity, and 14.3% assays showed low toxicity. The results obtained revealed that the studied genera of marine cyanobacteria are a promising source of novel compounds with potential anticancer activity and highlight the interest in also exploring the smaller filamentous and picoplanktonic genera of cyanobacteria. 

Exploring bioactive properties of marine cyanobacteria isolated from the Portuguese coast: high potential as a source of anticancer compounds.

For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates. We demonstrated the power of our approach by discriminating between two  strains in <30 min solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin, caused by a single frameshift mutation. Next, we used IDBac to detect subtle intraspecies differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwater  isolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we used IDBac to simultaneously extract protein and specialized metabolite MS profiles from unidentified Lake Michigan sponge-associated bacteria isolated from an agar plate. In just 3 h, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 spectra) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on interspecies and intraspecies differences in specialized metabolite production. IDBac is an attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow for facile discrimination of closely related bacterial colonies.

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function.

Marine sponges and cyanobacteria have a long history of co-evolution, with documented genome adaptations in cyanobionts. Both organisms are known to produce a wide variety of natural compounds, with only scarce information about novel natural compounds produced by cyanobionts. In the present study, we aimed to address their toxicological potential, isolating cyanobacteria ( = 12) from different sponge species from the coast of Portugal (mainland, Azores, and Madeira Islands). After large-scale growth, we obtained both organic and aqueous extracts to perform a series of ecologically-relevant bioassays. In the acute toxicity assay, using nauplii of , only organic extracts showed lethality, especially in picocyanobacterial strains. In the bioassay with , both organic and aqueous extracts produced embryogenic toxicity (respectively 58% and 36%), pointing to the presence of compounds that interfere with growth factors on cells. No development of pluteus larvae was observed for the organic extract of the strain  6MA13ti, indicating the presence of compounds that affect skeleton formation. In the hemolytic assay, none of the extracts induced red blood cells lysis. Organic extracts, especially from picoplanktonic strains, proved to be the most promising for future bioassay-guided fractionation and compounds isolation. This approach allows us to classify the compounds extracted from the cyanobacteria into effect categories and bioactivity profiles.

Article	Year
Exploring bioactive properties of marine cyanobacteria isolated from the Portuguese coast: high potential as a source of anticancer compounds. Marine drugs\| PubMed ID: 24384871	2013
Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 29686101	2018
Differential Toxicity of Cyanobacteria Isolated from Marine Sponges towards Echinoderms and Crustaceans. Toxins\| PubMed ID: 30021957	2018

Maria S. Costa

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