Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics

Abstract

Natural products (NPs) are a rich source of medicines, but traditional discovery methods are often unsuccessful due to high rates of rediscovery. Genetic approaches for NP discovery are promising, but progress has been slow due to the difficulty of identifying unique biosynthetic gene clusters (BGCs) and poor gene expression. We previously developed the metabologenomics method, which combines genomic and metabolomic data to discover new NPs and their BGCs. Here, we utilize metabologenomics in combination with molecular networking to discover a novel class of NPs, the tyrobetaines: nonribosomal peptides with an unusual trimethylammonium tyrosine residue. The BGC for this unusual class of compounds was identified using metabologenomics and computational structure prediction data. Heterologous expression confirmed the BGC and suggests an unusual mechanism for trimethylammonium formation. Overall, the discovery of the tyrobetaines shows the great potential of metabologenomics combined with molecular networking and computational structure prediction for identifying interesting biosynthetic reactions and novel NPs.

Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria

“…These genes encode for the enzymes involved in peptide assembly, regulation, resistance, and synthesis of a secondary metabolite, and are physically clustered into groups called biosynthetic gene clusters (BGCs) 10 . Recent studies involving mining of large-scale genomic datasets have highlighted the tremendous potential of discovering novel and potentially relevant compounds from microbes 9,[11][12][13] , which can allay some of the challenges in antibiotic development today 14,15 . While it has been estimated that many more novel natural products remain to be uncovered and functionally characterized, particularly those from poorly studied ecological niches, it is uncertain what the true number is or whether ongoing drug discovery efforts are reaching BGC saturation 16 .…”

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

“…BGC sequence similarity networks are then generated by applying a cut-off to the distance matrix calculated by BiG-SCAPE, while rounds of affinity propagation clustering 34 are used to group BGCs into GCFs, and GCFs into "Gene Cluster Clans" (GCCs). This process of categorization facilitates calculating metabologenomic correlations 35,36 at multiple levels. Results can be further processed in downstream analysis or immediately visualized using an interactive HTML-based interface that permits dynamic exploration of the gene cluster network (see further below for more details).…”

Refining and expanding nonribosomal peptide synthetase function and mechanism

“…Several cyclic NRPs from fungi are generated by an NRPS that terminates with a C domain in place of the TE domain that would typically be found in a bacterial NRPS. Biochemical studies of these NRPS systems have demonstrated that the C domains, which have been termed C T domains, catalyze intramolecular cyclization of the final aminoacyl-S-CP [40,20,77,34]. Structural investigation of the NRPSs involved in the biosynthesis of the indole alkaloid fumiquinazoline F have revealed that C T domains have an overall fold that is similar to the canonical C domains of bacterial NRPSs with a few key differences that help explain the unique intramolecular cyclization reaction [122].…”