Polyketide and nonribosomal peptide retro-biosynthesis and global gene cluster matching

Abstract

Polyketides (PKs) and nonribosomal peptides (NRPs) are profoundly important natural products, forming the foundations of many therapeutic regimes. Decades of research have revealed over 11,000 PK and NRP structures, and genome sequencing is uncovering new PK and NRP gene clusters at an unprecedented rate. However, only ∼10% of PK and NRPs are currently associated with gene clusters, and it is unclear how many of these orphan gene clusters encode previously isolated molecules. Therefore, to efficiently guide the discovery of new molecules, we must first systematically de-orphan emergent gene clusters from genomes. Here we provide to our knowledge the first comprehensive retro-biosynthetic program, generalized retro-biosynthetic assembly prediction engine (GRAPE), for PK and NRP families and introduce a computational pipeline, global alignment for natural products cheminformatics (GARLIC), to uncover how observed biosynthetic gene clusters relate to known molecules, leading to the identification of gene clusters that encode new molecules.

Breaking the silence: new strategies for discovering novel natural products

“…For example, an automated genomes-to-natural products platform (GNP) was recently developed to predict, combinatorialize and identify the product of modular gene clusters (PKS and NRPS) from LC-MS/MS of crude extracts [54 •• ]. In order to match the polyketides and nonribosomal peptides to their corresponding BGCs, they further developed generalized retro-biosynthetic assembly prediction engine (GRAPE) and global alignment for natural products cheminformatics (GARLIC) [55]. Besides processing the BGCs and MS/MS spectra individually, a new strategy was developed to group BGCs and MS/MS spectrums into gene cluster families (GCFs) and molecular families (MFs) by similarity [56].…”

Omics-based natural product discovery and the lexicon of genome mining

“…Both of these experimental approaches have unique challenges that vary with the organism being studied. Nonetheless, progress has been made in the automation of heterologous expression systems[16] and in retro-biosynthetic approaches to link orphan BGCs to known compounds[17] thus suggesting that this bottleneck may ultimately be overcome through advances in synthetic and computational biology. Meanwhile, the relatively few BGCs that have been experimentally characterized (1,393 BGCs in MIBiG as of May 2017) relative to the considerably larger number of microbial NPs discovered over the last 50-plus years (52,395 microbial NPs[18]) raises the generally understated possibility that much of the apparent genetic potential observed in bacterial genome sequences has already been realized.…”

Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production

“…[31] The GARLIC pipeline allows for both linking orphaned products to their corresponding BGCs and for identification of novel compounds by aligning bacterial PK and NRP BGCs predicted by PRISM to a comprehensive library of natural products from GRAPE. [30] The applicability of this pipeline consisting of PRISM, GRAPE, and GARLIC was Figure 3. Workflow of systems metabolic engineering for the optimal production of secondary metabolites.…”

“…[13,29] Upon LC-MS/MSguided identification of new compounds, following compound mining (or cheminformatic) tools enable automated compound characterization and dereplication: Global Alignment for natuRaL-products chemInformatiCs (GARLIC) in combination with Generalized Retrobiosynthetic Assembly Prediction Engine (GRAPE) platform [30] ; and the open-access MS/MS database Global Natural Products Social Molecular Networking (GNPS). [31] The GARLIC pipeline allows for both linking orphaned products to their corresponding BGCs and for identification of novel compounds by aligning bacterial PK and NRP BGCs predicted by PRISM to a comprehensive library of natural products from GRAPE.…”