Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster

Abstract

Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis. P. luminescens is a Gammaproteobacterium that undergoes phenotypic variation and can have both pathogenic and mutualistic roles. Through extensive gene deletion, pathway-targeted molecular networking, quantitative proteomic analysis, and NMR, we show that the genetic locus affects the regulation of quorum sensing and secondary metabolic enzymes and encodes new pteridine metabolites functionalized with cis-amide acyl-side chains, termed pepteridine A (1) and B (2). The pepteridines are produced in the pathogenic phenotypic variant and represent the first reported metabolites to be synthesized by a hybrid NRPS-pteridine pathway. These studies expand our view of the combinatorial biosynthetic potential available in bacteria.DOI: http://dx.doi.org/10.7554/eLife.25229.001

One‐carbon metabolism, folate, zinc and translation

“…In this family of scenarios, a thioester swinging arm, such as 4‐phosphopantetheine, would be involved in the polymerization of relevant metabolites, such as those generated today in non‐ribosomal peptide synthesis, polyketide synthesis or fatty acid synthesis (Lipmann, 1971), resulting in the synthesis of coenzymes, pterins in particular (Danchin, 2017a). While this latter view may appear far‐fetched, extant metabolism has identified in at least one case a bacterium displaying an explicit link between non‐ribosomal peptide synthesis and pteridine synthesis (Park et al , 2017). Nitrogen fixation had also to store nitrogen‐rich compounds, possibly as guanidinium skeleton‐containing metabolites.…”

Structure of a bound peptide phosphonate reveals the mechanism of nocardicin bifunctional thioesterase epimerase-hydrolase half-reactions

“…While the canonical biosynthesis carried out by NRPSs has been well-studied, an increasing number of examples exist in which NRPS domains are shown to catalyze unusual activities 4 . These activities include amide formation by adenylation domains 5,6 , condensation domain-catalyzed amide formation between a propionate and a pteridine ring in an unusual “pepteridine” natural product 7 , thioesterase domain-mediated condensation of two α-keto carboxylates in the production of quinone or furanone derivatives 8,9 , β-lactone and β-lactam cyclization by thioesterase domains 10–12 , and a Dieckmann condensation catalyzed by an unusual reductase domain, which lacks the conventional catalytic triad, involved in the release of cyclopiazonate tetramic acid neurotoxin 13 . Some of these activities reflect more limited changes in the overall synthetic program, for example, the use of an alternate nucleophile to attack the adenylate directly in formation of the amide bond that bypasses the PCP-bound thioester intermediate.…”

Heterologous expression of bacterial natural product biosynthetic pathways

“…76 Crawford and colleagues identied two new pteridine metabolites, pepteridine A (46) and B (47), as well as the known 7,8-dihydroxanthopterin and pterin by heterologous expression of a hybrid NRPS-pteridine genomic island from the entomopathogen Photorhabdus luminescens TT01 in E. coli BAP1 under the control of a phage T7 promoter. 169 In addition, Nihira et al discovered a novel diol-containing PKS lavendiol 48 from Streptomyces lavendulae by expressing the unique BGC of such streptenolfamily compounds. 170 This established the heterologous platform for the rational design of novel lavendiol derivatives for further bioactivity screening.…”