Trapping of a Polyketide Synthase Module after C-C Bond Formation Reveals Transient Acyl Carrier Domain Interactions.

Modular polyketide synthases (PKSs) are giant assembly lines that produce an impressive range of biologically active compounds. However, our understanding of the structural dynamics of these megasynthases, specifically the delivery of acyl carrier protein (ACP)-bound building blocks to the catalytic site of the ketosynthase (KS) domain, remains severely limited. Using a multipronged structural approach, we report details of the inter-domain interactions after C-C bond formation in a chain-branching module of the rhizoxin PKS. Mechanism-based crosslinking of an engineered module was achieved using a synthetic substrate surrogate that serves as a Michael acceptor. The crosslinked protein allowed us to identify an asymmetric state of the dimeric protein complex upon C-C bond formation by cryo-electron microscopy (cryo-EM). The possible existence of two ACP binding sites, one of them a potential "parking position" for substrate loading, was also indicated by AlphaFold2 predictions. NMR spectroscopy showed that a transient complex is formed in solution, independent of the linker domains, and photochemical crosslinking/mass spectrometry of the standalone domains allowed us to pinpoint the interdomain interaction sites. The structural insights into a branching PKS module arrested after C-C bond formation allows a better understanding of domain dynamics and provides valuable information for the rational design of modular assembly lines.

A Modular In†Vitro Platform for the Production of Terpenes and Polyketides from CO2.

A long-term goal in realizing a sustainable biocatalysis and organic synthesis is the direct use of the greenhouse gas CO2 as feedstock for the production of bulk and fine chemicals, such as pharmaceuticals, fragrances and food additives. Here we developed a modular in vitro platform for the continuous conversion of CO2 into complex multi-carbon compounds, such as monoterpenes (C10 ), sesquiterpenes (C15 ) and polyketides. Combining natural and synthetic metabolic pathway modules, we established a route from CO2 into the key intermediates acetyl- and malonyl-CoA, which can be subsequently diversified through the action of different terpene and polyketide synthases. Our proof-of-principle study demonstrates the simultaneous operation of different metabolic modules comprising of up to 29 enzymes in one pot, which paves the way for developing and optimizing synthesis routes for the generation of complex CO2 -based chemicals in the future.

Understanding Substrate Selectivity of Phoslactomycin Polyketide Synthase by Using Reconstituted in Vitro Systems.

Polyketide synthases (PKSs) use simple extender units to synthesize complex natural products. A fundamental question is how different extender units are site-specifically incorporated into the growing polyketide. Here we established phoslactomycin (Pn) PKS, which incorporates malonyl- and ethylmalonyl-CoA, as an in vitro model to study substrate specificity. We combined up to six Pn PKS modules with different termination sites for the controlled release of tetra-, penta- and hexaketides, and challenged these systems with up to seven different extender units in competitive assays to test for the specificity of Pn modules. While malonyl-CoA modules of Pn PKS exclusively accept their natural substrate, the ethylmalonyl-CoA module PnC tolerates different α-substituted derivatives, but discriminates against malonyl-CoA. We show that the ratio of extender transacylation to hydrolysis controls incorporation in PnC, thus explaining site-specific selectivity and promiscuity in the natural context of Pn PKS.

On-Line Polyketide Cyclization into Diverse Medium-Sized Lactones by a Specialized Ketosynthase Domain.

Ketosynthase (KS) domains of modular type I polyketide synthases (PKSs) typically catalyze the Claisen condensation of acyl and malonyl units to form linear chains. In stark contrast, the KS of the rhizoxin PKS branching module mediates a Michael addition, which sets the basis for a pharmacophoric δ-lactone moiety. The precise role of the KS was evaluated by site-directed mutagenesis, chemical probes, and biotransformations. Biochemical and kinetic analyses helped to dissect branching and lactonization reactions and unequivocally assign the entire sequence to the KS. Probing the range of accepted substrates with diverse synthetic surrogates in vitro, we found that the KS tolerates defined acyl chain lengths to produce five- to seven-membered lactones. These results show that the KS is multifunctional, as it catalyzes ß-branching and lactonization. Information on the increased product portfolio of the unusual, TE-independent on-line cyclization is relevant for synthetic biology approaches.

Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification.

Terpenoid natural products comprise a wide range of molecular architectures that typically result from C-C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes.

On-line enzymatic tailoring of polyketides and peptides in thiotemplate systems.

Non-ribosomal peptide synthetases (NRPS) and type I polyketide synthases (PKS) are versatile thiotemplate systems for the programmed assembly of biosynthetic building blocks. Typically, the post-PKS/NRPS enzymes tailor the resulting chains to yield the bioactive natural product scaffolds. However, more and more examples have surfaced showing that important structural modifications take place while the intermediates are still bound to the assembly line. A growing number of enzymatic domains and trans-acting enzymes as well as their recruiting areas in the modules have been identified and characterized. In addition to the widespread on-line alkylations, hydroxylations and heterocyclizations into oxazole/thiazole residues, on-line modifications lead to a variety of ring systems such as cycloethers, lactones, lactams, glutarimides, cyclopropanes, decalins and cyclic biaryls.

Polyketide synthase chimeras reveal key role of ketosynthase domain in chain branching.

Biosynthesis of rhizoxin in Burkholderia rhizoxinica affords an unusual polyketide synthase module with ketosynthase and branching domains that install the δ-lactone, conferring antimitotic activity. To investigate their functions in chain branching, we designed chimeric modules with structurally similar domains from a glutarimide-forming module and a dehydratase. Biochemical, kinetic and mutational analyses reveal a structural role of the accessory domains and multifarious catalytic actions of the ketosynthase.

Twofold polyketide branching by a stereoselective enzymatic Michael addition.

The versatility of the branching module of the rhizoxin polyketide synthase was tested in an in vitro enzyme assay with a polyketide mimic and branched (di)methylmalonyl-CoA extender units. Comparison of the products with synthetic reference compounds revealed that the module is able to stereoselectively introduce two branches in one step by a Michael addition-lactonisation sequence, thus expanding the scope of previously studied PKS systems.

Enzymatic polyketide chain branching to give substituted lactone, lactam, and glutarimide heterocycles.

Polyketides typically result from head-to-tail condensation of acyl thioesters to produce highly functionalized linear chains. The biosynthesis of the phytotoxin rhizoxin, however, involves a polyketide synthase (PKS) module that introduces a δ-lactone chain branch through Michael addition of a malonyl extender to an α,ß-unsaturated intermediate unit. To evaluate the scope of the branching module, polyketide mimics were synthesized and their biotransformation by the reconstituted PKS module from the Rhizopus symbiont Burkholderia rhizoxinica was monitored in vitro. The impact of the type and configuration of the δ-substituents was probed and it was found that amino-substituted surrogates yield the corresponding lactams. A carboxamide analogue was transformed into a glutarimide unit, which can be found in many natural products. Our findings illuminate the biosynthesis of glutarimide-bearing polyketides and also demonstrate the utility of this branching module for synthetic biology.

The first nonradioactive fluorescence assay for phosphatidylglycerol:prolipoprotein diacylglyceryl transferase that initiates bacterial lipoprotein biosynthesis.

The unique and physiologically vital bacterial enzyme, prolipoprotein diacylglyceryl transferase (Lgt), which catalyzes the committed first step in the posttranslational transfer of diacylglyceryl group from phosphatidylglycerol to the prospective N-terminal cysteine of prolipoproteins, remains to be characterized for want of a simpler but equally sensitive nonradioactive assay. We, for the first time, report a coupled enzymatic fluorescence assay for Lgt using the de novo synthetic peptide substrate MKATKSAVGSTLAGCSSHHHHHH. The assay is based on the conversion of the by-product, glycerol-1-phosphate, to dihydroxyacetone using an alkaline phosphatase-glycerol dehydrogenase combination and estimating the fluorescence of the coupled reduction of resazurin to resorufin. The minimum amount of glycerol-1-phosphate, and hence the modified peptide, detected by this method is approximately 20pmol, thereby making this assay a promising alternative to the radioactive assays. The assay is rapid, more convenient, less laborious, and suitable for purification and characterization of Lgt.