Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer

Abstract

For more than half a century the pharmaceutical industry has sifted through natural products produced by microbes, uncovering new scaffolds and fashioning them into a broad range of vital drugs. We sought a strategy to reinvigorate the discovery of natural products with distinctive structures using bacterial genome sequencing combined with metabolomics. By correlating genetic content from 178 actinomycete genomes with mass spectrometry-enabled analyses of their exported metabolomes, we paired new secondary metabolites with their biosynthetic gene clusters. We report the use of this new approach to isolate and characterize tambromycin, a new chlorinated natural product, composed of several nonstandard amino acid monomeric units, including a unique pyrrolidine-containing amino acid we name tambroline. Tambromycin shows antiproliferative activity against cancerous human B- and T-cell lines. The discovery of tambromycin via large-scale correlation of gene clusters with metabolites (a.k.a. metabologenomics) illuminates a path for structure-based discovery of natural products at a sharply increased rate.

Modern mass spectrometry for synthetic biology and structure-based discovery of natural products

“…53-55 In fact, this method can be paired with matching isotope patterns for de novo chemical formula determination, which is particularly helpful when dealing with an unknown compound and beginning a full structure determination. 56,57 …”

Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations

“…13,14 When metabologenomics is applied to actinomycetes, a rich source of microbial natural products, 15 the method provides a new screen for active secondary metabolism. 13 Thus, despite the extensive efforts of the natural products research community to characterize actinomycetes natural products, these organisms still contain a trove of new scaffolds and enzymes.…”

Biosynthetic Genes for the Tetrodecamycin Antibiotics

“…These include glycosylated compounds (32), nonribosomal peptides (33), enediynes (34), phosphonates (35), and halogenated compounds (36). Identifying related clusters in multiple organisms is also becoming a widely accepted means of informatically characterizing a new gene cluster (for example, the cluster associated with tambromycin [37]). This has particular value in identifying the edges of the cluster, a process that classically involves disrupting genes at the predicted edges of the cluster.…”