Moonlighting Metals: Insights into Regulation of Cyclization Pathways in Fungal Δ6‐Protoilludene Sesquiterpene Synthases

Fungal 1,11 cyclizing sesquiterpene synthases are product specific under typical reaction conditions. However, in vivo expression of certain Δ⁶‐protoilludene synthases results in dual 1,11 and 1,10 cyclization. To determine the factors regulating this mechanistic variation, in‐depth in vitro characterization of Δ⁶‐protoilludene synthases was conducted. Divalent metal ions determine cyclization specificity and this product variability. Promiscuity in metal binding is mediated by secondary metal‐binding sites away from the conserved D(D/E)XX(D/E) motif in sesquiterpene synthases. Phylogenetic analysis revealed a divergent evolution of Basidiomycota trans‐humulyl cation producing sesquiterpene synthases, results that indicate a wider diversity in function than previously predicted. This study provides key insights into the function and evolution of 1,11 cyclizing fungal sesquiterpene synthases.     

Sesquiterpene Synthases Cop4 and Cop6 from Coprinus cinereus: Catalytic Promiscuity and Cyclization of Farnesyl Pyrophosphate Geometric Isomers

Sesquiterpene synthases catalyze with different catalytic fidelity the cyclization of farnesyl pyrophosphate (FPP) into hundreds of known compounds with diverse structures and stereochemistries. Two sesquiterpene synthases, Cop4 and Cop6, were previously isolated from Coprinus cinereus as part of a fungal genome survey. This study investigates the reaction mechanism and catalytic fidelity of the two enzymes. Cyclization of all‐trans‐FPP ((E,E)‐FPP) was compared to the cyclization of the cis–trans isomer of FPP ((Z,E)‐FPP) as a surrogate for the secondary cisoid neryl cation intermediate generated by sesquiterpene synthases, which are capable of isomerizing the C2? C3 π bond of all‐trans‐FPP. Cop6 is a “high‐fidelity” α‐cuprenene synthase that retains its fidelity under various conditions tested. Cop4 is a catalytically promiscuous enzyme that cyclizes (E,E)‐FPP into multiple products, including (?)‐germacrene D and cubebol. Changing the pH of the reaction drastically alters the fidelity of Cop4 and makes it a highly selective enzyme. Cyclization of (Z,E)‐FPP by Cop4 and Cop6 yields products that are very different from those obtained with (E,E)‐FPP. Conversion of (E,E)‐FPP proceeds via a (6R)‐β‐bisabolyl carbocation in the case of Cop6 and an (E,E)‐germacradienyl carbocation in the case of Cop4. However, (Z,E)‐FPP is cyclized via a (6S)‐β‐bisabolene carbocation by both enzymes. Structural modeling suggests that differences in the active site and the loop that covers the active site of the two enzymes might explain their different catalytic fidelities.     

Discovery of the Tiancilactone Antibiotics by Genome Mining of Atypical Bacterial Type II Diterpene Synthases

Although genome mining has advanced the identification, discovery, and study of microbial natural products, the discovery of bacterial diterpenoids continues to lag behind. Herein, we report the identification of 66 putative producers of novel bacterial diterpenoids, and the discovery of the tiancilactone (TNL) family of antibiotics, by genome mining of type II diterpene synthases that do not possess the canonical DXDD motif. The TNLs, which are broad‐spectrum antibiotics with moderate activities, are produced by both Streptomyces sp. CB03234 and Streptomyces sp. CB03238 and feature a highly functionalized diterpenoid skeleton that is further decorated with chloroanthranilate and γ‐butyrolactone moieties. Genetic manipulation of the tnl gene cluster resulted in TNL congeners, which provided insights into their biosynthesis and structure–activity relationships. This work highlights the biosynthetic potential that bacteria possess to produce diterpenoids and should inspire continued efforts to discover terpenoid natural products from bacteria.     

Exploration and mining of the bacterial terpenome

Tens of thousands of terpenoids are present in both terrestrial and marine plants, as well as fungi. In the last 5-10 years, however, it has become evident that terpenes are also produced by numerous bacteria, especially soil-dwelling Gram-positive organisms such as Streptomyces and other Actinomycetes. Although some microbial terpenes, such as geosmin, the degraded sesquiterpene responsible for the smell of moist soil, the characteristic odor of the earth itself, have been known for over 100 years, few terpenoids have been identified by classical structure- or activity-guided screening of bacterial culture extracts. In fact, the majority of cyclic terpenes from bacterial species have only recently been uncovered by the newly developed techniques of "genome mining". In this new paradigm for biochemical discovery, bacterial genome sequences are first analyzed with powerful bioinformatic tools, such as the BLASTP program or Profile Hidden Markov models, to screen for and identify conserved protein sequences harboring a characteristic set of universally conserved functional domains typical of all terpene synthases. Of particular importance is the presence of variants of two universally conserved domains, the aspartate-rich DDXX(D/E) motif and the NSE/DTE triad, (N/D)DXX(S/T)XX(K/R)(D/E). Both domains have been implicated in the binding of the essential divalent cation, typically Mg(2+), that is required for cyclization of the universal acyclic terpene precursors, such as farnesyl and geranyl diphosphate. The low level of overall sequence similarity among terpene synthases, however, has so far precluded any simple correlation of protein sequence with the structure of the cyclized terpene product. The actual biochemical function of a cryptic bacterial (or indeed any) terpene synthase must therefore be determined by direct experiment. Two common approaches are (i) incubation of the expressed recombinant protein with acyclic allylic diphosphate substrates and identification of the resultant terpene hydrocarbon or alcohol and (ii) in vivo expression in engineered bacterial hosts that can support the production of terpene metabolites. One of the most attractive features of the coordinated application of genome mining and biochemical characterization is that the discovery of natural products is directly coupled to the simultaneous discovery and exploitation of the responsible biosynthetic genes and enzymes. Bacterial genome mining has proved highly rewarding scientifically, already uncovering more than a dozen newly identified cyclic terpenes (many of them unique to bacteria), as well as several novel cyclization mechanisms. Moreover, bioinformatic analysis has identified more than 120 presumptive genes for bacterial terpene synthases that are now ripe for exploration. In this Account, we review a particularly rich vein we have mined in the genomes of two model Actinomycetes, Streptomyces coelicolor and Streptomyces avermitilis, from which the entire set of terpenoid biosynthetic genes and pathways have now been elucidated. In addition, studies of terpenoid biosynthetic gene clusters have revealed a wealth of previously unknown oxidative enzymes, including cytochromes P450, non-heme iron-dependent dioxygenases, and flavin monooxygenases. We have shown that these enzymes catalyze a variety of unusual biochemical reactions, including two-step ketonization of methylene groups, desaturation-epoxidation of secondary methyl groups, and pathway-specific Baeyer-Villiger oxidations of cyclic ketones.     

Sesquiterpene Synthase‐Catalysed Formation of a New Medium‐Sized Cyclic Terpenoid Ether from Farnesyl Diphosphate Analogues

Terpene synthases catalyse the first step in the conversion of prenyl diphosphates to terpenoids. They act as templates for their substrates to generate a reactive conformation, from which a Mg²⁺‐dependent reaction creates a carbocation–PP_i ion pair that undergoes a series of rearrangements and (de)protonations to give the final terpene product. This tight conformational control was exploited for the (R)‐germacrene A synthase– and germacradien‐4‐ol synthase–catalysed formation of a medium‐sized cyclic terpenoid ether from substrates containing nucleophilic functional groups. Farnesyl diphosphate analogues with a 10,11‐epoxide or an allylic alcohol were efficiently converted to a 11‐membered cyclic terpenoid ether that was characterised by HRMS and NMR spectroscopic analyses. Further experiments showed that other sesquiterpene synthases, including aristolochene synthase, δ‐cadinene synthase and amorphadiene synthase, yielded this novel terpenoid from the same substrate analogues. This work illustrates the potential of terpene synthases for the efficient generation of structurally and functionally novel medium‐sized terpene ethers.     

Nucleophilic Water Capture or Proton Loss: Single Amino Acid Switch Converts δ‐Cadinene Synthase into Germacradien‐4‐ol Synthase

δ‐Cadinene synthase is a sesquiterpene cyclase that utilises the universal achiral precursor farnesyl diphosphate (FDP) to generate predominantly the bicyclic sesquiterpene δ‐cadinene and about 2 % germacradien‐4‐ol, which is also generated from FDP by the cyclase germacradien‐4‐ol synthase. Herein, the mechanism by which sesquiterpene synthases discriminate between deprotonation and reaction with a nucleophilic water molecule was investigated by site‐directed mutagenesis of δ‐cadinene synthase. If W279 in δ‐cadinene synthase was replaced with various smaller amino acids, the ratio of alcohol versus hydrocarbon product was directly proportional to the van der Waals volume of the amino acid side chain. DCS‐W279A is a catalytically highly efficient germacradien‐4‐ol synthase (k_cat/K_M=1.4×10^?3 μm s^?1) that produces predominantly germacradien‐4‐ol in addition to 11 % δ‐cadinene. Water capture is not achieved through strategic positioning of a water molecule in the active site, but through a coordinated series of loop movements that allow bulk water access to the final carbocation in the active site prior to product release.     

An Iterative O‐Methyltransferase Catalyzes 1,11‐Dimethylation of Aspergillus fumigatus Fumaric Acid Amides

S‐adenosyl‐l ‐methionine (SAM)‐dependent methyltransfer is a common biosynthetic strategy to modify natural products. We investigated the previously uncharacterized Aspergillus fumigatus methyltransferase FtpM, which is encoded next to the bimodular fumaric acid amide synthetase FtpA. Structure elucidation of two new A. fumigatus natural products, the 1,11‐dimethyl esters of fumaryl‐l ‐tyrosine and fumaryl‐l ‐phenylalanine, together with ftpM gene disruption suggested that FtpM catalyzes iterative methylation. Final evidence that a single enzyme repeatedly acts on fumaric acid amides came from an in vitro biochemical investigation with recombinantly produced FtpM. Size‐exclusion chromatography indicated that this methyltransferase is active as a dimer. As ftpA and ftpM homologues are found clustered in other fungi, we expect our work will help to identify and annotate natural product biosynthesis genes in various species.     

Chlorinative Cyclization of 1,6‐Enynes by Enantioselective Palladium(II)/Palladium(IV) Catalysis

A novel asymmetric catalysis via a palladium(II)/palladium(IV) cycle has been developed by utilizing a chiral spiro bis(isoxazoline) ligand (SPRIX). Intramolecular chlorinative cyclization of 1,6‐enynes catalyzed by a palladium‐SPRIX complex proceeded enantioselectively to afford α‐methylene‐γ‐lactone derivatives.     

A Practical Asymmetric Synthesis of Enantiopure Spiro[4,4]nonane‐1,6‐dione

A practical asymmetric synthesis of enantiopure spiro[4,4]nonane‐1,6‐dione, a valuable precursor for chiral ligand development, is reported. This synthetic strategy includes a kinetic resolution of the readily synthesized ketone precursor with a chiral quaternary carbon center by bioreduction with baker’s yeast as the key step, followed by a hydroformylation, oxidation, esterification and Dieckmann cyclization reaction sequence to generate the spiro five‐membered ring. It was found that the masking of the β‐ketone carbonyl group of enantiopure ethyl 1‐allyl‐2‐oxocyclopentanecarboxylate via formation of a ketal with 1,3‐diol derivative is necessary during the process of Dieckmann condensation in order to prevent its racemization under basic conditions. This method allows the gram‐scale preparation of both enantiomers of spiro[4,4]nonane‐1,6‐dione ( 1 ) with excellent enantiopurities (up to >99% ee) in the overall yields of 54% [(R)‐ 1 ] and 42% [(S)‐ 1 ], respectively. The practicality of the present synthetic procedure has provided a fundamental platform for the development of spiro[4,4]nonane‐1,6‐dione‐based chiral chemistry.     

Rhodium‐Catalyzed Asymmetric Pauson–Khand Reaction Using Monophosphoramidite Ligand SIPHOS

A novel rhodium‐catalyzed asymmetric intramolecular Pauson–Khand reaction using a chiral monophosphoramidite ligands is described. In this reaction, an in situ generated catalyst from [Rh(CO)₂Cl]₂, the spiro‐monophosphoramidite ligand SIPHOS and AgSbF₆ was found to be effective for a series of 1,6‐enynes, providing the co‐cyclization products in good enantioselectivities (84% ee).     

Terpene Synthases in the Biosynthesis of Drimane-Type Sesquiterpenes across Diverse Organisms

Drimane-type sesquiterpenes (DTSs) are significant terpenoid natural products characterized by their unique C₁₅ bicyclic skeleton. They are produced by various organisms including plants, fungi, bacteria and marine organisms, and exhibit a diverse array of bioactivities. These bioactivities encompass antifeedant, anti-insecticidal, anti-bacterial, anti-fungal, anti-viral and anti-proliferative properties. Some DTSs contribute to the pungent flavor found in herb plants like water pepper, while others serve as active components responsible for the anti-cancer activities observed in medicinal mushrooms such as (−)-antrocin from Antrodia cinnamomea. Recently, DTS synthases have been identified in various organisms, biosynthesizing drimenol, drim-8-ene-11-ol and (+)-albicanol, which all possess the characteristic drimane skeleton. Interestingly, despite these enzymes producing chemical molecules with a drimane scaffold, they exhibit minimal amino acid sequence identity across different organisms. This Concept article focuses on the discovery of DTS synthases and the tailoring enzymes generating the chemical diversity of drimane natural products. We summarize and discuss their key features, including the chemical mechanisms, catalytic motifs and functional domains employed by these terpene synthases to generate DTS scaffolds.     

Chemoselectivity in the Pd‐Catalyzed Cyclization of 1,6‐Enynes and Proof of the Relative Configuration of the New Stereogenic Centers

The dimerization of dienyne 6 with a palladole catalyst readily provides the bicyclic enyne rac‐ 7 . A second cyclization of the 1,6‐enyne substructure in rac‐ 7 works best with a hydropalladation catalyst and delivers rac‐ 8 . Diels‐Alder reactions of the latter finally lead to a crystalline product rac‐ 12 . A crystal structure analysis of rac‐ 12 allowed the determination of the relative configuration of all stereogenic centers formed in the dimerization of 6 .     

Ribosomal Synthesis of Natural‐Product‐Like Bicyclic Peptides in Escherichia coli

Methods to access natural‐product‐like macrocyclic peptides can disclose new opportunities for the exploration of this important structural class for chemical biology and drug discovery applications. Here, the scope and mechanism of a novel strategy for directing the biosynthesis of thioether‐bridged bicyclic peptides in bacterial cells was investigated. This method entails split intein‐catalyzed head‐to‐tail cyclization of a ribosomally produced precursor peptide, combined with inter‐side‐chain crosslinking through a genetically encoded cysteine‐reactive amino acid. This strategy could be successfully applied to achieve formation of structurally diverse bicyclic peptides with high efficiency and selectivity in Escherichia coli. Insights into the sequence of reactions underlying the peptide bicyclization process were gained from time‐course experiments. Finally, the potential utility of this methodology toward the discovery of macrocyclic peptides with enhanced functional properties was demonstrated through the isolation of a bicyclic peptide with sub‐micromolar affinity for streptavidin.     

Cyclopropyl Building Blocks for Organic Synthesis, 131. Palladium‐Catalyzed Bicyclization with Carbonyl Insertion of Alkenyl‐Tethered Propargyl Carbonates Towards a Scalable Synthesis of Various 2‐(Bicyclo[3.1.0]hex‐1‐yl)acrylates

The Pd‐catalyzed 5‐exo‐trig‐3‐exo‐trig cascade cyclization of 1,6‐enynes with a propargyl carbonate terminus offers the shortest synthetic route to variously substituted 2‐(bicyclo[3.1.0]hex‐1‐yl)acrylates, a novel class of prospective monomers for low‐shrinkage polymers. To apply this reaction to large‐scale preparations of the said bicyclic acrylates, a flexible Pd catalyst system with tunable reactivity has been developed. The dependence of the product and diastereomer distribution on both the reaction conditions, including the type of palladium catalyst used, and on the nature of the substrate has been investigated. A variety of methyl 2‐(bicyclo[3.1.0]hex‐1‐yl)acrylates and parent carboxylic acids as well as some of their derivatives of potential interest towards a technical application were prepared on a multigram scale. A general large‐scale synthesis of the cyclization precursors bearing one or two carbonyl groups in the tether is also disclosed.     

Efficient and Selective Rhodium‐Catalyzed Hydrophosphorylation of Dienes

The hydrophosphorylation of a model 1,6‐diene having a terminal and an internal alkene function has been investigated. Free radical protocols lead invariably to mixtures of cyclic phosphonate products, due to rapid cyclization of the intermediary radical species. Rhodium catalysis using a cyclic pinacol‐derived phosphonate provides an efficient technique for the highly selective (>99 %) hydrophosphorylation at the terminal alkene function. In situ modification of Wilkinson’s complex by addition of 2–50 equivalents (vs. Rh) of a monophosphine (PCy₃>PPh₃) or carbene ligand greatly improves the catalyst performances (TON up to 2250 mol phosphonate/mol Rh). An even more efficient system was obtained with 2 equivalents (vs. Rh) of the bidentate 1,6‐bis(diphenylphosphino)hexane ligand, which affords so far unprecedented high catalytic productivity (TON up to 4 550 mol phosphonate/mol Rh) and activity (TOF up to 250 h⁻¹).     

Diesters of diols in wheat leaf wax

Diesters have been isolated from the leaf wax of spring wheat,Triticum aestivum, L. (Selkirk variety) by chromatography. The diesters, which form 3% of the wax and which were shown by gas liquid chromatography to be a mixture of C₅₁−C₆₀ esters, consist largely oftrans 2-docosenoic andtrans 2-tetracosenoic acid esters of 1,9-nonanediol, 1,10-decanediol, 1,11-undecanediol and 1,12-dodecanediol. The structures of the components were confirmed by synthesis. Issued as NRCC No. 12064     

Impedance spectroscopy of N‐substituted oligo‐oxyethylene polypyrrole films

The electrochemical properties of neutral (dedoped) and oxidized (doped) poly(1,11‐bis(1,1‐pyrrole)‐3,6,9‐trioxaundecane) (poly‐ I ) film electrodes were investigated using cyclic voltammetry and electrochemical impedance spectroscopy (EIS) techniques. Poly‐ I was deposited on glassy carbon electrode (GCE) from acetonitrile solution containing 5.0 × 10^?3M 1,11‐bis(1,1‐pyrrole)‐3,6,9‐trioxaundecane ( I ) and 0.1M LiClO₄ supporting electrolyte. Doped poly‐ I exhibits a single semicircle in its complex‐capacitance plots, indicating a single dominant ion transport process, together with high capacitance values. These features make this polymer film a candidate for an energy storage material. Also, poly‐ I can be a candidate as a sensory material for the detection of Ag⁺ based on impedance parameters. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci 2008     

Two Triterpene Synthases from Imperata cylindrica Catalyzing the Formation of a Pair of Diastereoisomers through Boat or Chair Cyclization

Imperata cylindrica is known to produce a pair of triterpenes, isoarborinol and fernenol, that exhibit identical planar structures but possess opposite stereochemistry at six of the nine chiral centers. These differences arise from a boat or a chair cyclization of the B-ring of the substrate. Herein, we report the characterization of three OSC genes from I. cylindrica. IcOSC1 and IcOSC5 were identified as isoarborinol and fernenol synthases, respectively, while IcOSC3 was characterized as a multifunctional enzyme that produces glutinol and friedelin as its major products. Mutational studies of isoarborinol and fernenol synthases revealed that the residues surrounding the DCTAE motif partially affected the conformation of the B-ring during cyclization. Additionally, the IcOSC1-W255H mutant produced the rare triterpene boehmerol. The introduced histidine residue presumably abstracted a proton from the intermediary carbocation at C18 during the 1,2-rearrangement. Expression analysis indicated that all OSC genes were highly expressed in stems.     

Bioactivity‐Guided Genome Mining Reveals the Lomaiviticin Biosynthetic Gene Cluster in Salinispora tropica

The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico‐chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo‐ and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB‐440 by a DNA interference bioassay to isolate DNA‐targeting enediyne polyketides. An organic extract of S. tropica showed DNA‐interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA‐interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.     

Five‐Membered Cyclitol Phosphate Formation by a myo‐Inositol Phosphate Synthase Orthologue in the Biosynthesis of the Carbocyclic Nucleoside Antibiotic Aristeromycin

Aristeromycin is a unique carbocyclic nucleoside antibiotic produced by Streptomyces citricolor. In order to elucidate its intriguing carbocyclic formation, we used a genome‐mining approach to identify the responsible enzyme. In silico screening with known cyclitol synthases involved in primary metabolism, such as myo‐inositol‐1‐phosphate synthase (MIPS) and dehydroqunate synthase (DHQS), identified a unique MIPS orthologue (Ari2) encoded in the genome of S. citricolor. Heterologous expression of the gene cluster containing ari2 with a cosmid vector in Streptomyces albus resulted in the production of aristeromycin, thus indicating that the cloned DNA region (37.5 kb) with 33 open reading frames contains its biosynthetic gene cluster. We verified that Ari2 catalyzes the formation of a novel five‐membered cyclitol phosphate from d ‐fructose 6‐phosphate (F6P) with NAD⁺ as a cofactor. This provides insight into cyclitol phosphate synthase as a member of the MIPS family of enzymes. A biosynthetic pathway to aristeromycin is proposed based on bioinformatics analysis of the gene cluster.