Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus

Abstract

Despite an excellent track record, microbial drug discovery suffers from high rates of rediscovery. Better workflows for the rapid investigation of complex extracts are needed to increase throughput and to allow early prioritization of samples. In addition, systematic characterization of poorly explored strains is seldomly performed. Here, we report a metabolomic study of 72 isolates belonging to the rare actinomycete genus Planomonospora , using a workflow of commonly used open access tools to investigate its secondary metabolites. The results reveal a correlation of chemical diversity and strain phylogeny, with classes of metabolites exclusive to certain phylogroups. We were able to identify previously reported Planomonospora metabolites, including the ureylene-containing oligopeptide antipain, the thiopeptide siomycin including new congeners, and the ribosomally synthesized peptides sphaericin and lantibiotic 97518. In addition, we found that Planomonospora strains can produce the siderophore desferrioxamine or a salinichelin-like peptide. Analysis of the genomes of three newly sequenced strains led to the detection of 59 gene cluster families, of which three were connected to products found by LC-MS/MS profiling. This study demonstrates the value of metabolomic studies to investigate poorly explored taxa and provides a first picture of the biosynthetic capabilities of the genus Planomonospora .

Comparative Metabologenomics Analysis of Polar Actinomycetes

“…Targeted linking and automated approaches for accelerating drug discovery have been reviewed [39,53]. Recently, metabolomic and genomic data of 72 isolates belonging to the rare actinomycete genus Planomonospora were analysed using publicly available tools to link specialised metabolites to their corresponding BGCs [77]. The authors were able to manually pair siomycin congeners to a RiPP BGC and a new salinichelin-like metabolite to the known BGC encoding for erythrochelin.…”

Integrating perspectives in actinomycete research: an ActinoBase review of 2020–21

“…Stemming from metabolomic studies of Planomonospora strains from Naicons' strain collection [101], Zdouc et al purified and elucidated the structure of a novel tripeptide with an unusual carbon-carbon (C-C) bond between amino acids. The authors propose to call this novel class of compounds biarylitides, since the products feature a C-C bridge between the aromatic amino acid residues.…”

Allopeptimicins: unique antibacterial metabolites generated by hybrid PKS-NRPS, with original self-defense mechanism in Actinoallomurus

“…6,7 Particularly promising is the combination of metabolomic tools to poorly explored bacterial taxa. In recent work on bacterial strains belonging to the actinobacterial genus Planomonospora, we uncovered novel chemistry, which led to a family of unexpected biosynthetic gene clusters (BGCs), 8,9 which in turn helped uncover further novel chemistry. 10 We previously reported that strains belonging to another actinobacterial genus, Actinoallomurus, produce at high frequency molecules with antibacterial activity, 11 with several new variants of known scaffolds identified through bioactivity-based screening.…”

“…6,7 Particularly promising is the combination of metabolomic tools to poorly explored bacterial taxa. In recent work on bacterial strains belonging to the actinobacterial genus Planomonospora , we uncovered novel chemistry, which led to a family of unexpected biosynthetic gene clusters (BGCs), 8,9 which in turn helped uncover further novel chemistry. 10…”