Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced byStreptomycesSpecies MBT28

Abstract

Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by Streptomyces sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (1) with antimicrobial activity against Bacillus subtilis. The metabolite-guided genome mining of Streptomyces sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics.

Comparative metabolomics reveals defence‐related modification of citrinin by Penicillium citrinum within a synthetic Penicillium–Pseudomonas community

“…PLS here acted as a supervised data reduction algorithm to study the correlation of the abundances of these 40 mass features ( X ‐variables) in total with exchange rate values ( Y ‐variables). A permutation test that is a calculation of quality of the fit and the predictive ability validated the supervised model (Wu et al ., ). The R 2 and Q 2 values for this PLS analysis were 0.98 and 0.88, respectively, indicating a favourable predictability and reproducibility.…”

Aromatic Polyketide GTRI‐02 is a Previously Unidentified Product of theactGene Cluster inStreptomyces coelicolor A3(2)

“…2D NMR examination of co‐culture crude extracts confirmed that these two singlets belong to the same compound. NMR‐guided chromatographic fractionation was carried out to isolate the desired components . Fractions showing the target signals ( δ =2.45 and 2.42 ppm) were combined and further analyzed by 2 D NMR, including by COSY, 1 J ‐resolved, HSQC, and HMBC (Figures S1–S5 in the Supporting Information).…”

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

“…222-225 However, low abundance compounds can often be overlooked in complex extracts, and recently MVSA have been utilized to help link observed fraction bioactivity to detectable features from metabolomic analyses. 39,226 Even after correlating metabolites with biological activity, determining the mode of action for active compounds can be difficult and expensive. 227-230 One approach has been developed that uses the antibiotic spectrum of activities across different organisms, mode of action profiles (BioMAP), to group similar antibiotics.…”