Molecular Networking-Guided Discovery and Characterization of Stechlisins, a Group of Cyclic Lipopeptides from a Pseudomonas sp.

Abstract

Increasingly sensitive analytical instruments and robust downstream data processing tools have revolutionized natural product research over the past decade. A molecular networking-guided survey led to the identification of 33 new cyclic lipopeptides (CLPs) from the culture broth of the proteobacterium Pseudomonas sp. FhG100052. The compound family resembles members of the amphisin group of CLPs that possess a 3-hydroxy fatty acid linked to the N-terminus of an undecapeptide core. Culture optimization led to the isolation and subsequent structure elucidation of one known and five new derivatives by extensive MS/MS and NMR experiments in combination with Marfey’s analysis. The data were in agreement with in silico analysis of the corresponding biosynthetic gene cluster. Most strikingly, the length of the incorporated fatty acid defined the growth inhibitory effects against Moraxella catarrhalis FH6810, as observed by MIC values ranging from no inhibition (>128 μg/mL) to 4 μg/mL.

Identification, Characterization and Synthesis of Natural Parasitic Cysteine Protease Inhibitors – More Potent Falcitidin Analogs

“…A visualization of the network was constructed in Cytoscape v3.6.0. 46 Edges were drawn between scan nodes with a cosine similarity >0.7 47 . Samples were dissolved in 100 µL H2O, derivatized with L-FDVA and analyzed using the same parameters as described before.…”

Sustainable Low-Volume Analysis of Environmental Samples by Semi-Automated Prioritization of Extracts for Natural Product Research (SeaPEPR)

“…While these results indicate a generally robust transfer of primarily observed growth inhibitory effects to microfractionated assays, two extracts did not show bioactivity in any fraction. These findings emphasize a general challenge in bioactivity driven NP research (in contrast to cheminformatics inclined discovery projects [38]): Microbial crude extracts are composed of a mixture of various substances at dramatically different concentrations and potencies. It is important to realize that almost each substance (or a combination of several metabolites) becomes unspecifically toxic at high concentrations, hence producing a positive assay read out.…”

“…MSConvert (ProteoWizard package32) was used to convert the raw data (*.d files) into plain text (*.mgf) files, wherein all detected fragment ions are expressed as a list of mass/intensity value pairs sorted according to their parent ions (peak picking: vendor MS level = 1-2; threshold type = absolute intensity, value = 1000, orientation = most-intense). The networking algorithm itself, thus the calculation of cosine similarity values between parent ion vectors, was computed offline, using an in house server [38].…”

Transporter Gene-Mediated Typing for Detection and Genome Mining of Lipopeptide-Producing Pseudomonas

“…The accession numbers for NRPS genes and PleB and PvdT homologs are provided in Table S1. Tensin congeners produced by strain FhG100052 were designated stechlisins ( 10 ).…”

“…LPs are also involved in important ecological functions, such as swarming motility, biofilm formation, phytopathogenicity, cooperation, or antagonism ( 3 – 5 ). In recent years, research on Pseudomonas LPs has grown rapidly and many studies reported new producer strains of known LPs as well as the characterization of new LPs among single or large sets of environmental Pseudomonas isolate(s) ( 6 – 10 ). The initial detection of LP producer strains often relies on phenotypical tests (e.g., surfactant, antagonistic, or hemolytic activities) or on DNA amplification targeting conserved catalytic domains in their biosynthetic enzymes, complemented with analytical chemistry methodologies (e.g., liquid chromatography-mass spectrometry [LC-MS]).…”