< Back to previous page

Dataset

Replication Data for: Charting the lipopeptidome of non-pathogenic Pseudomonas

A major source of pseudomonad specialized metabolites are the non-ribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with - but not restricted to - phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in non-pathogenic Pseudomonas genomes, covering thirteen chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin-family members (nepenthesin, oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in fifteen (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin- and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges.
Publication year:2022
Accessibility:open
Publisher:KU Leuven RDR
License:CC-BY-NC-ND-4.0
Format:pdf, xlsx
Keywords: Biosynthetic Gene Clusters (BGC), Cyclic Lipopeptides (CLPs), Genome mining, Lipopeptidome, NMR Fingerprint Matching, Non-Ribosomal Peptide Synthetases (NRPS), Phylogeny, Pseudomonas, rpoD