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Tropone natural products are non‐benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA‐bound precursor featuring a seven‐membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA‐release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture., Accidents will happen: The biosynthesis of bacterial tropone natural products depends on an unusual intertwining of primary and secondary metabolism. Remarkably, a shunt product arising from a “metabolic accident” of an aromatic catabolic pathway serves as universal precursor for tropone natural products.

The structural diversity of type II polyketides is largely generated by tailoring enzymes. In rishirilide biosynthesis by Streptomyces bottropensis, 13C-labeling studies previously implied extraordinary carbon backbone and side-chain rearrangements. In this work, we employ gene deletion experiments and in vitro enzyme studies to identify key biosynthetic intermediates and expose intricate redox tailoring steps for the formation of rishirilides A, B, and D and lupinacidin A. First, the flavin-dependent RslO5 reductively ring-opens the epoxide moiety of an advanced polycyclic intermediate to form an alcohol. Flavin monooxygenase RslO9 then oxidatively rearranges the carbon backbone, presumably via lactone-forming Baeyer-Villiger oxidation and subsequent intramolecular aldol condensation. While RslO9 can further convert the rearranged intermediate to rishirilide D and lupinacidin A, an additional ketoreductase RslO8 is required for formation of the main products rishirilide A and rishirilide B. This work provides insight into the structural diversification of aromatic polyketide natural products via unusual redox tailoring reactions that appear to defy biosynthetic logic.

Natural products are distinct and often highly complex organic molecules that constitute not only an important drug source, but have also pushed the field of organic chemistry by providing intricate targets for total synthesis. How the astonishing structural diversity of natural products is enzymatically generated in biosynthetic pathways remains a challenging research area, which requires detailed and sophisticated approaches to elucidate the underlying catalytic mechanisms. Commonly, the diversification of precursor molecules into distinct natural products relies on the action of pathway-specific tailoring enzymes that catalyze, e.g., acylations, glycosylations, or redox reactions. This review highlights a selection of tailoring enzymes that employ riboflavin (vitamin B2)-derived cofactors (FAD and FMN) to facilitate unusual redox catalysis and steer the formation of complex natural product pharmacophores. Remarkably, several such recently reported flavin-dependent tailoring enzymes expand the classical paradigms of flavin biochemistry leading, e.g., to the discovery of the flavin-N5-oxide - a novel flavin redox state and oxygenating species.

Ever since the discovery of the flavin cofactor more than 80 years ago, flavin-dependent enzymes have emerged as ubiquitous and versatile redox catalysts in primary metabolism. Yet, the recent advances in the discovery and characterization of secondary metabolic pathways exposed new roles for flavin-mediated catalysis in the generation of structurally complex natural products. Here, we review a selection of key biosynthetic flavoenzymes from marine bacterial secondary metabolism and illustrate how their functional and mechanistic investigation expanded our view of the cofactor's chemical repertoire and led to the discovery of a previously unknown flavin redox state.

The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O 2 ) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O 2 , as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O 2 -pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O 2 within a flavoenzyme’s active site enables the regiospecific formation of a covalent flavin–oxygen adduct and oxygenating species (i.e., the flavin-N5-oxide) by mimicking a critical transition state. This study unambiguously demonstrates how enzymes may control the O 2 functionalization of an organic cofactor as prerequisite for oxidative catalysis. Our work thus illustrates how O 2 reactivity can be harnessed in an enzymatic environment and provides crucial knowledge for future rational design of O 2 -reactive enzymes.

Flavoenzymes are versatile catalysts that mostly facilitate redox reactions such as the oxygenation of organic substrates. Commonly, flavin monooxygenases employ a flavin-C4a-(hydro)peroxide as oxygenating species. Recently, however, a modified N5-functionalized flavin cofactor featuring a distinct nitrone moiety — the flavin-N5-oxide — was reported for the first time as oxygenating species in the bacterial enzyme EncM that catalyzes the dual oxidation of a reactive poly-β-ketone substrate. Meanwhile, additional flavoenzymes have been reported that form the flavin-N5-oxide. Here, we highlight aspects of the discovery and characterization of this novel flavin redox state with a focus on recent findings that shed more light onto its chemical features and enzymatic formation. We furthermore provide a rationale for the oxygenase functionality of EncM by contrast with structurally related flavin oxidases and dehydrogenases from the vanillyl alcohol oxidase/p-cresol methylhydroxylase flavoprotein (VAO/PCMH) superfamily. In addition, the possible biological roles of the flavin-N5-oxide are discussed.

Terpenoids are ubiquitous in nature and exhibit an immense structural diversity. Commonly, terpenoid biosynthesis involves prenyl diphosphate synthases (terpene synthases) that produce linear prenyl diphosphates with various chain lengths via conventional “head-to-tail” coupling of C5 units. Structural diversification, in contrast, is often mediated by terpene cyclases and additional tailoring enzymes. Recently, however, a few unusual prenyl diphosphate synthases were reported that catalyze noncanonical “head-to-torso” coupling reactions and thus formation of various branched prenyl diphosphates such as isosesquilavandulyl diphosphate. Here, I describe these enzymes in detail and illustrate how these branching reactions are key to formation of various structurally distinct natural products such as the complex polycyclic merochlorin antibiotics from a marine bacterium.

The vanadium-dependent chloroperoxidase Mcl24 was discovered to mediate a complex series of unprecedented transformations in the biosynthesis of the merochlorin meroterpenoid antibiotics. In particular, a site-selective naphthol chlorination is followed by a sequence of oxidative dearomatization/terpene cyclization reactions to build up the stereochemically complex carbon framework of the merochlorins in one step. Inspired by the enzyme reactivity, we developed a chemical chlorination protocol paralleling the biocatalytic process. These chemical studies led to the identification of previously overlooked merochlorin natural products.

The polycycles merochlorin A and B are complex halogenated meroterpenoid natural products with significant antibacterial activities and are produced by the marine bacterium Streptomyces sp. strain CNH-189. Heterologously produced enzymes and chemical synthesis are employed herein to fully reconstitute the merochlorin biosynthesis in vitro. The interplay of a dedicated type III polyketide synthase, a prenyl diphosphate synthase, and an aromatic prenyltransferase allow formation of a highly unusual aromatic polyketide-terpene hybrid intermediate which features an unprecedented branched sesquiterpene moiety from isosesquilavandulyl diphosphate. As supported by in vivo experiments, this precursor is furthermore chlorinated and cyclized to merochlorin A and isomeric merochlorin B by a single vanadium-dependent haloperoxidase, thus completing the remarkably efficient pathway.

Structural and functional studies reveal how the bacterial flavoenzyme EncM catalyses the oxygenation–dehydrogenation dual oxidation of a highly reactive substrate, and show that EncM maintains a stable flavin oxygenating species that promotes substrate oxidation and triggers a rarely seen Favorskii-type rearrangement. Flavoproteins, which contain either a flavin adenine dinucleotide or a flavin mononucleotide cofactor, are redox-active proteins involved in a broad range of biological processes including bioluminescence, photosynthesis and DNA repair. Here the authors undertook structural and functional studies to examine how the bacterial flavoenzyme EncM catalyses the oxygenation–dehydrogenation oxidation of a highly reactive substrate. They observed previously unknown flavin redox biochemistry: EncM maintains a stable flavin-oxygenating species that promotes substrate oxidation and triggers a rarely seen, Favorskii-type rearrangement that is central to the biosynthesis of the marine antibiotic enterocin. Flavoproteins catalyse a diversity of fundamental redox reactions and are one of the most studied enzyme families1,2. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate1,3,4. Here we report that the bacterial flavoenzyme EncM5,6 catalyses the peroxyflavin-independent oxygenation–dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics and isotope labelling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unexpected stable flavin-oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization.

Heterologous expression of secondary metabolic pathways is a promising approach for the discovery and characterization of bioactive natural products. Herein we report the first heterologous expression of a natural product from the model marine actinomycete genus Salinispora. Using the recently developed method of yeast-mediated transformation-associated recombination for natural product gene clusters, we captured a type II polyketide synthase pathway from Salinispora pacifica with high homology to the enterocin pathway from Streptomyces maritimus and successfully produced enterocin in two different Streptomyces host strains. This result paves the way for the systematic interrogation of Salinispora’s promising secondary metabolome.