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Nat Microbiol. 2016 Oct 31;2:16197. doi: 10.1038/nmicrobiol.2016.197.

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.

Author information

1
Department of Chemistry and Biochemistry, University of California San Diego, California 92093, USA.
2
Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, California 92093, USA.
3
Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan.
4
Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
5
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, California 92093, USA.
6
Ion Torrent by Thermo Fisher, 5781 Van Allen Way, Carlsbad, California 92008, USA.
7
Centre of Microbial and Plant Genetics, KU Leuven, 3001 Heverlee, Belgium.
8
Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708PB Wageningen, The Netherlands.
9
Department of Ecology and Evolutionary Biology, University of California, 1156 High Street, Santa Cruz, California 95064, USA.
10
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, California 92093, USA.
11
Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
12
School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
13
Department of AgroEcology, Rothamsted Research, West Common, Harpenden AL5 2JQ, UK.

Abstract

Pseudomonads are cosmopolitan microorganisms able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density and enhance or inhibit growth of competing microorganisms. However, these valuable metabolites are typically characterized one-molecule-one-microbe at a time, instead of being inventoried in large numbers. To index and map the diversity of molecules detected from these organisms, 260 strains of ecologically diverse origins were subjected to mass-spectrometry-based molecular networking. Molecular networking not only enables dereplication of molecules, but also sheds light on their structural relationships. Moreover, it accelerates the discovery of new molecules. Here, by indexing the Pseudomonas specialized metabolome, we report the molecular-networking-based discovery of four molecules and their evolutionary relationships: a poaeamide analogue and a molecular subfamily of cyclic lipopeptides, bananamides 1, 2 and 3. Analysis of their biosynthetic gene cluster shows that it constitutes a distinct evolutionary branch of the Pseudomonas cyclic lipopeptides. Through analysis of an additional 370 extracts of wheat-associated Pseudomonas, we demonstrate how the detailed knowledge from our reference index can be efficiently propagated to annotate complex metabolomic data from other studies, akin to the way in which newly generated genomic information can be compared to data from public databases.

PMID:
27798598
PMCID:
PMC5538791
DOI:
10.1038/nmicrobiol.2016.197
[Indexed for MEDLINE]
Free PMC Article

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