Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

Abstract

Empedopeptins—eight amino acid cyclic lipopeptides—are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

“…This species exists in a taxonomic limbo since the original species description lacks a complete etymology and strain ATCC 31962 T is no longer available. ATCC 31962 T was connected to an expired patent (US patent 4,409,210) involving production of the depsipeptide antibiotic empedopeptin while strain YMA4 forms a novel polyyne antifungal compound [34]. Results here confirm Miess et al .…”

“…Nomenclatural descriptions are indicated below while phenotypic details are provided in the original description papers. Also located in the Pseudoduganella armeniaca subgroup is the atypically salt-tolerant species '[Empedobacter] haloabium' [32,33], represented by ATCC 31962 T and by another strain YMA4 [34] (Table S1). This species exists in a taxonomic limbo since the original species description lacks a complete etymology and strain ATCC 31962 T is no longer available.…”

Molecular Networking‐Guided Discovery of Kyonggic Acids in Massilia spp.

“…Mass features corresponding to massiliachelin, [8] massinidine, [8] and violacein [7] were exclusively found in culture extracts of Massilia sp. NR 4-1, whereas mass features corresponding to massiliamide [4] or empedopeptins [5] were completely missing. Although this result does not rule out a possible production under different fermentation conditions than those used in this study, it adds evidence to the assumption of a largely strain-specific secondary metabolome in the genus Massilia.…”

“…Although its biosynthetic potential was recognized in previous genomic analyses, [3] only three Massilia strains have actually been explored with regard to the production of secondary metabolites. These investigations led to the discovery of cyclic peptides, namely massiliamide [4] and the empedopeptins, [5] as well as alkaloids, including the structurally unusual massinidine [6] and the bisindole violacein. [7] The latter two compounds were isolated from a biosynthetically particularly talented strain, Massilia sp.…”

Discovery, Biosynthetic Origin, and Heterologous Production of Massinidine, an Antiplasmodial Alkaloid

“…NR 4-1 isolated from a plant-associated soil sample was selected for investigation, as its culture extract showed activity in an antiplasmodial bioassay. Although genomic analyses had already indicated Massilia species as promising sources of bioactive NPs, , only little is actually known regarding the chemistry of these bacteria. , The culture extract from strain NR 4-1 was fractionated on a reversed-phase C 18 HPLC column, and the collected fractions were submitted sequentially to antiplasmodial activity tests and LC/MS analyses. This tandem procedure led to the detection of a bioactive compound ( 1 ) with a molecular ion at m / z 240.1492 [M + H] + .…”