Enzymology of acyl chain macrocyclization in natural product biosynthesis

Polyketides and nonribosomal peptides constitute a large and diverse set of natural products with biological activity in microbial survival and pathogenesis, as well as broad pharmacological utility as antineoplastics, antibiotics or immunosupressants. These molecules are biosynthesized by the ordered condensation of monomer building blocks, acyl-CoAs or amino acids, leading to construction of linear acyl chains. Many of these natural products are constrained to their bioactive conformations by macrocyclization whereby, in one of the terminal steps of biosynthesis, parts of the molecule distant in the constructed linear acyl chain are covalently linked to one another. Typically, macrocyclization is catalyzed by a thioesterase domain at the C-terminal end of the biosynthetic assembly line, although alternative strategies are known. The enzymology of these macrocyclization catalysts, their structure, mechanism, and catalytic versatility, is the subject of this review. The diversity of macrocyclic structures accessed by enzyme catalyzed cyclization of linear acyl chains as well as their inherent substrate tolerance suggests their potential utility in reprogramming natural product biosynthesis pathways or accessing novel macrocyclic structures.     

Structural evidence for an enolate intermediate in GFP fluorophore biosynthesis

The Aequorea victoria green fluorescent protein (GFP) creates a fluorophore from its component amino acids Ser65, Tyr66, and Gly67 through a remarkable post-translational modification, involving spontaneous peptide backbone cyclization, dehydration, and oxidation reactions. Here we test and extend the understanding of fluorophore biosynthesis by coupling chemical reduction and anaerobic methodologies with kinetic analyses and protein structure determination. Two high-resolution structures of dithionite-treated GFP variants reveal a previously uncharacterized enolate intermediate form of the chromophore that is viable in generating a fluorophore (t1/2 = 39 min-1) upon exposure to air. Isolation of this enolate intermediate will now allow specific probing of the rate-limiting oxidation step for fluorophore biosynthesis in GFP and its red fluorescent protein homologues. Such targeted characterizations may lead to the design of faster maturing proteins with enhanced applications in biotechnology and cell biology. Moreover, our results reveal how the GFP protein environment mimics enzyme systems, by stabilizing an otherwise high energy enolate intermediate to achieve its post-translational modification.     

Investigations in the field of acyl group carriers

Conclusions Two representatives of phosphate ester derivatives of pantothenonitrile have been obtained: the methyl ester of D-(+)-4-C-[2-O-mesylpantothenonitrilyloxy(phenoxy)phosphonyl]-N-benzyloxycarbonylserine and the ethyl ester of D-(+)-4-C-[2-O-mesylpantothenonitrilyl(phenoxy)phosphonyl]-N-benzyloxycarbonylserylglycine.Khimiya Prirodnykh Soedinenii, Vol. 5, No. 3, pp. 174–176, 1969     

O-nucleophilic features of amidoximes in acyl group transfer reactions

Analysis of kinetic behavior of isomeric Z-amidoximes and their Z-ions in reactions with 4-nitrophenyl-4-toluenesulfonate, diethylphosphate, and diethylphosphonate was performed in the framework of Bronsted relationship. The reactivity of amidoximate anions with respect to the mentioned substrates is comparable to that of typical -nucleophiles, oximate ions. The -effect decreased with the growing basicity of amidoximate ions, and for compounds with pK _a>12.0 it was totally lacking. The high nucleophilic activity of neutral amidoximes and their anionic forms was ascribed to the cyclic structure of the transition state involving two kinds of assistance: general acidic, and basic catalysis. A unique feature of amidoximes as -nucleophiles consists in their ability to perform efficient cleavage of ecotoxic substrates in a wide pH range, from basic to acid media.Translated from Zhurnal Organicheskoi Khimii, Vol. 40, No. 11, 2004, pp. 1665–1677.Original Russian Text Copyright © 2004 by Prokopeva, Simanenko, Karpichev, Savelova, Popov.     

Promiscuous fatty acyl CoA ligases produce acyl-CoA and acyl-SNAC precursors for polyketide biosynthesis

The study of bioactive natural products has undergone rapid advancement with the cloning and sequencing of large number of gene clusters and the concurrent progress to manipulate complex biosynthetic systems in heterologous hosts. The genetic reconstitution necessitates that the heterologous hosts possess substrate pools that could be coordinately supplied for biosynthesis. Polyketide synthases (PKS) utilize acyl-coenzyme A (CoA) precursors and synthesize polyketides by repetitive decarboxylative condensations. Here we show that acyl-CoA ligases, which belong to a large family of acyl-activating enzymes, possess potential to produce varied starter CoA precursors that could be utilized in polyketide biosynthesis. Incidentally, such protein domains have been recognized in several PKS and nonribosomal peptide synthetase gene clusters. Our studies with mycobacterial fatty acyl-CoA ligases (FACLs) show remarkable tolerance to activate a variety of fatty acids that contain modifications at alpha, beta, omega, and omega-nu positions. This substrate flexibility extends further such that these proteins also efficiently utilize N-acetyl cysteamine, the shorter acceptor terminal portion of CoASH, to produce acyl-SNACs. We show that the in situ generated acyl-CoAs and acyl-SNACs could be channeled to types I and -III PKS systems to produce new metabolites. Together, the promiscuous activity of FACL and PKSs provides new opportunities to expand the repertoire of natural products.     

Cucurbitadienol synthase, the first committed enzyme for cucurbitacin biosynthesis, is a distinct enzyme from cycloartenol synthase for phytosterol biosynthesis

Three oxidosqualene cyclase (OSC) cDNAs (CPX, CPQ, CPR) were cloned from seedlings of Cucurbita pepo by homology based PCR method. Their open reading frames were expressed in lanosterol synthase deficient (erg7) Saccharomyces cerevisiae strain GIL77. Analyses of in vitro enzyme activities and in vivo accumulated products in the transformants demonstrated that CPQ and CPX encode cucurbitadienol and cycloartenol synthases, respectively. These results indicated the presence of distinct OSCs for cycloartenol and cucurbitadienol synthesis in this plant.     

Effects of reaction temperature and acyl group for lipase-catalyzed chiral binaphthol synthesis

Candida antarctica lipase-catalyzed hydrolysis of O-butyryl-BINOL [(±)-3] or O-butyryl-6,6′-dibromo-BINOL [(±)-5] yielded optically active BINOL [(R)-1] or 6,6′-dibromo-BINOL [(R)-4] with high enantiomeric excess at 80 °C. Reaction temperature and acyl group of substrate had a great influence on the reactivity and enantioselectivity, respectively, of lipase-catalyzed hydrolysis for chiral binaphthol synthesis.     

Rapid identification of enzyme variants for reengineered alkaloid biosynthesis in periwinkle

Monoterpene indole alkaloids from Catharanthus roseus (Madagascar periwinkle), such as the anticancer agents vinblastine and vincristine, have important pharmacological activities. Metabolic engineering of alkaloid biosynthesis can provide an efficient and environmentally friendly route to analogs of these synthetically challenging and pharmaceutically valuable natural products. However, the narrow substrate scope of strictosidine synthase, the enzyme at the entry point of the pathway, limits a pathway engineering approach. We demonstrate that with a different expression system and screening method it is possible to rapidly identify strictosidine synthase variants that accept tryptamine analogs not turned over by the wild-type enzyme. The variants are used in stereoselective synthesis of beta-carboline analogs and are assessed for biosynthetic competence within the terpene indole alkaloid pathway. These results present an opportunity to explore metabolic engineering of "unnatural" product production in the plant periwinkle.     

The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis

Acyl carrier protein (ACP) plays an essential role in fatty acid and polyketide biosynthesis, and most of the fatty acid synthases (FASs) and polyketide synthases (PKSs) known to date are characterized with a single ACP for each cycle of chain elongation. Polyunsaturated fatty acid (PUFA) biosynthesis is catalyzed by the PUFA synthase, and all PUFA synthases known to date contain tandem ACPs (ranging from 5 to 9). Using the Pfa PUFA synthase from Shewanella japonica as a model system, we report here that these tandem ACPs are functionally equivalent regardless of their physical location within the PUFA synthase subunit, but the total number of ACPs controls the overall PUFA titer. These findings set the stage to interrogate other domains and subunits of PUFA synthase for their roles in controlling the final PUFA products and could potentially be exploited to improve PUFA production.     

Imidazole as a catalyst in acyl transfer. A model enzyme system for physiological transacetylation

The transfer of an acyl group from glucose penta-acetate to methanol, n-amylamine, and n-amyl mercaptan with imidazole catalysis has been observed and studied with the aid of PMR spectroscopy. Through rate studies of the reaction between glucose penta-acetate and methanol in the presence of imidazole, and as a result of the observation of imidazole-catalyzed epimerization of β- to -glucose penta-acetate, a mechanism for the transacetylation reaction has been proposed. The possibility that this mechanism can be applied to enzyme catalyzed physiological transacetylations is discussed.     

Redesign of a central enzyme in alkaloid biosynthesis

Plant alkaloids exhibit a diverse array of structures and pharmaceutical activities, though metabolic engineering efforts in these eukaryotic pathways have been limited. Strictosidine synthase (STR) is the first committed step in the biosynthesis of over two thousand terpene indole alkaloids. We describe a rational redesign of the STR binding pocket to selectively accommodate secologanin substrate analogs. The mutant is selective for a substrate that can be chemoselectively derivatized. Evidence that this substrate can be processed by later steps of the terpene indole alkaloid pathway is provided. The work demonstrates that the central enzyme of this alkaloid pathway can be redesigned and that the pathway can turn over the unnatural intermediate that is generated. Modulation of the substrate specificity of enzymes of this complex pathway is therefore likely to enable metabolic engineering efforts of these alkaloids.     

The berberine bridge forming enzyme in tetrahydroprotoberberine biosynthesis

The enzyme responsible for the berberine bridge formation was purified to homogeneity and shown to catalyze, in the presence of oxygen, the conversion of (S)-reticuline, (S)-protosinomenine and (S)-laudanosoline to the correspondingly substituted (S)-tetrahydroprotoberberines and stoichiometric amounts of H₂O₂     

7-Chloroquinoline: a versatile intermediate for the synthesis of 7-substituted quinolines

A practical synthesis of 7-mono-substituted quinolines has been achieved. Selective reduction of the inexpensive commercial reagent 4,7-dichloroquinoline affords 7-chloroquinoline, which has been converted into more complex 7-mono-substituted quinolines through a series of Pd-catalyzed cross coupling reactions. These studies include the first examples of Suzuki reactions for the preparation of 7-mono-substituted quinolines as well as the first application of the Sonagashira reaction for the synthesis of 7-substituted quinolines. This strategy has been extended to the preparation of 2,7-di-substituted quinolines.     

Dihydrophenylalanine: a prephenate-derived Photorhabdus luminescens antibiotic and intermediate in dihydrostilbene biosynthesis

2,5-Dihydrophenylalanine (H(2)Phe) is a multipotent nonproteinogenic amino acid produced by various Actinobacteria and Gammaproteobacteria. Although the metabolite was discovered over 40 years ago, details of its biosynthesis have remained largely unknown. We show here that L-H(2)Phe is a secreted metabolite in Photorhabdus luminescens cultures and a precursor of a recently described 2,5-dihydrostilbene. Bioinformatic analysis suggested?a candidate gene cluster for the processing of prephenate to H(2)Phe, and gene knockouts validated that three adjacent genes plu3042-3044 were required for H(2)Phe production. Biochemical experiments validated Plu3043 as a nonaromatizing prephenate decarboxylase generating an endocyclic dihydro-hydroxyphenylpyruvate. Plu3042 acted next to transaminate the Plu3043 product, precluding spontaneous exocyclic double-bond isomerization and yielding 2,5-dihydrotyrosine. The enzymatic products most plausibly on path to H(2)Phe illustrate the versatile metabolic rerouting of prephenate from aromatic amino acid synthesis to antibiotic synthesis.     

Mechanism of migration of an acyl group in the pyrrole ring of indole

The isomerization of deuterium-labeled (in position 3) 2-acylindoles in polyphosphoric and trifluoroacetic acids was studied. It is shown that migration of the acyl group from position 2 to position 3 is accompanied by an intramolecular hydride shift.Deceased.Translated from Khimiya Geterotsoklicheskikh Soedinenii, No. 9, pp. 1235–1238, September, 1980.