Domain-Targeted Metabolomics Delineates the Heterocycle Assembly Steps of Colibactin Biosynthesis

Abstract

Modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) comprise giant multidomain enzymes responsible for the “assembly line” biosynthesis of many genetically encoded small molecules. Site-directed mutagenesis, protein biochemical, and structural studies have focused on elucidating the catalytic mechanisms of individual multidomain proteins and protein domains within these megasynthases. However, probing their functions at the cellular level typically has invoked the complete deletion (or overexpression) of multidomain-encoding genes or combinations of genes and comparing those mutants with a control pathway. Here we describe a “domain-targeted” metabolomic strategy that combines genome editing with pathway analysis to probe the functions of individual PKS and NRPS catalytic domains at the cellular metabolic level. We apply the approach to the bacterial colibactin pathway, a genotoxic NRPS–PKS hybrid pathway found in certain Escherichia coli. The pathway produces precolibactins, which are converted to colibactins by a dedicated peptidase, ClbP. Domain-targeted metabolomics enabled the characterization of “multidomain signatures”, or functional readouts of NRPS–PKS domain contributions to the pathway-dependent metabolome. These multidomain signatures provided experimental support for individual domain contributions to colibactin biosynthesis and delineated the assembly line timing events of colibactin heterocycle formation. The analysis also led to the structural characterization of two reactive precolibactin metabolites. We demonstrate the fate of these reactive intermediates in the presence and absence of ClbP, which dictates the formation of distinct product groups resulting from alternative cyclization cascades. In the presence of the peptidase, the reactive intermediates are converted to a known genotoxic scaffold, providing metabolic support of our mechanistic model for colibactin-induced genotoxicity. Domain-targeted metabolomics could be more widely used to characterize NRPS–PKS pathways with unprecedented genetic and metabolic precision.

Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway

“…Additionally, a recent report demonstrated the effect of ClbQ on the production yields of upstream and downstream precolibactin intermediates. 23,27 In one study, the Δ clbPQ strain produced higher yields of late-stage intermediates and aided in the isolation of the advanced metabolite 16 . 23 Taken together these studies suggest ClbQ plays an important regulatory role in colibactin production and cytotoxic activity.…”

Nonribosomal peptide synthetase biosynthetic clusters of ESKAPE pathogens

“…A recent proposal suggests that the timing of the hydrolysis of the acylasparagine leader may in fact lead to different precolibactin molecules, including pyridone forms such as ( 10 ) that do not react with DNA, as well as lactam ( 11 ) that is able to cross-link DNA. 174, 177 …”

ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance

“…9 This substrate is the N -methylamide analog of metabolite 1 , which was detected in clbP -encoding bacterial cultures in vivo and which has also been characterized by synthesis. 10 The structures of fully-elaborated (pre)-colibactins, accounting for all of the genes in the clb gene cluster, are unknown. Owing to its ease of organic extraction, 2 was used for analytical and preparative purposes.…”