Metabolomic and genomic investigation into the actinomycete genus Planomonospora

Bacteria belonging to the order of Actinomycetales are the source of many clinically important drugs, especially antibiotics. Due to the large back-catalogue of molecules isolated from these bacteria, it is difficult to find novel compounds by using traditional methods and sources. In this thesis, we use state-of-the-art metabolomics and genomics techniques to identify new molecules from the “rare actinomycete” genus Planomonospora. In chapter 2, we discuss methods for the differentiation of known and unknown molecules, called dereplication, in detail. Further, we describe the creation of a computationally predicted tandem mass fragmentation library from a proprietary metabolite database, which can speed up and automate the identification of known compounds. In chapter 3, we discuss our study into the “rare actinomycete” genus Planomonospora. We correlate phylogenetic diversity with metabolite diversity, showing that specific groups of strains produce specific molecules. Further, we sequence the genomes of selected strains to gain insight into their theoretical biosynthetic capacity. Eventually, we establish criteria to rationally select metabolites with a high probability of novelty, for consecutive isolation. In chapter 4, we describe the characterization of a family of novel metabolites, prioritized in the previous study. Investigation of the biosynthetic pathway suggests that the metabolite is a ribosomally synthesized and post-translationally modified peptide. Indeed, we prove that a minimal, two-gene biosynthetic gene cluster is responsible for the production of the compound. One of the two genes is, to our knowledge, the shortest peptide-encoding gene ever reported. This work can be the steppingstone for future investigations into the under-appreciated genus Planomonospora in particular and “rare actinomycetes” in general.