Prenyltransferases as key enzymes in primary and secondary metabolism

The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems

Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.

PrenDB, a Substrate Prediction Database to Enable Biocatalytic Use of Prenyltransferases

Prenyltransferases of the dimethylallyltryptophan synthase (DMATS) superfamily catalyze the attachment of prenyl or prenyl-like moieties to diverse acceptor compounds. These acceptor molecules are generally aromatic in nature and mostly indole or indole-like. Their catalytic transformation represents a major skeletal diversification step in the biosynthesis of secondary metabolites, including the indole alkaloids. DMATS enzymes thus contribute significantly to the biological and pharmacological diversity of small molecule metabolites. Understanding the substrate specificity of these enzymes could create opportunities for their biocatalytic use in preparing complex synthetic scaffolds. However, there has been no framework to achieve this in a rational way. Here, we report a chemoinformatic pipeline to enable prenyltransferase substrate prediction. We systematically catalogued 32 unique prenyltransferases and 167 unique substrates to create possible reaction matrices and compiled these data into a browsable database named PrenDB. We then used a newly developed algorithm based on molecular fragmentation to automatically extract reactive chemical epitopes. The analysis of the collected data sheds light on the thus far explored substrate space of DMATS enzymes. To assess the predictive performance of our virtual reaction extraction tool, 38 potential substrates were tested as prenyl acceptors in assays with three prenyltransferases, and we were able to detect turnover in >55% of the cases. The database, PrenDB (www.kolblab.org/prendb.php), enables the prediction of potential substrates for chemoenzymatic synthesis through substructure similarity and virtual chemical transformation techniques. It aims at making prenyltransferases and their highly regio- and stereoselective reactions accessible to the research community for integration in synthetic work flows.

Keeping It All Going-Complement Meets Metabolism

The complement system is an evolutionary old and crucial component of innate immunity, which is key to the detection and removal of invading pathogens. It was initially discovered as a liver-derived sentinel system circulating in serum, the lymph, and interstitial fluids that mediate the opsonization and lytic killing of bacteria, fungi, and viruses and the initiation of the general inflammatory responses. Although work performed specifically in the last five decades identified complement also as a critical instructor of adaptive immunity—indicating that complement’s function is likely broader than initially anticipated—the dominant opinion among researchers and clinicians was that the key complement functions were in principle defined. However, there is now a growing realization that complement activity goes well beyond “classic” immune functions and that this system is also required for normal (neuronal) development and activity and general cell and tissue integrity and homeostasis. Furthermore, the recent discovery that complement activation is not confined to the extracellular space but occurs within cells led to the surprising understanding that complement is involved in the regulation of basic processes of the cell, particularly those of metabolic nature—mostly via novel crosstalks between complement and intracellular sensor, and effector, pathways that had been overlooked because of their spatial separation. These paradigm shifts in the field led to a renaissance in complement research and provide new platforms to now better understand the molecular pathways underlying the wide-reaching effects of complement functions in immunity and beyond. In this review, we will cover the current knowledge about complement’s emerging relationship with the cellular metabolism machinery with a focus on the functional differences between serum-circulating versus intracellularly active complement during normal cell survival and induction of effector functions. We will also discuss how taking a closer look into the evolution of key complement components not only made the functional connection between complement and metabolism rather “predictable” but how it may also give clues for the discovery of additional roles for complement in basic cellular processes.

gem-Diprenylation of Acylphloroglucinols by a Fungal Prenyltransferase of the Dimethylallyltryptophan Synthase Superfamily

Aspergillus terreus aromatic prenyltransferase (AtaPT) catalyzes predominantly C-monoprenylation of acylphloroglucinols in the presence of different prenyl diphosphates. With dimethylallyl diphosphate (DMAPP) as prenyl donor, gem-diprenylated products 1D3, 2D3, and 3D3 were also detected. High conversion of 1D1 to 1D3, 2D1 to 2D3, and 3D1 to 3D3 was demonstrated by incubation with AtaPT and DMAPP. The first example of gem-diprenylation by a member of the dimethylallyltryptophan synthase superfamily is provided.

Biosynthesis of Shearinine: Diversification of a Tandem Prenyl Moiety of Fungal Indole Diterpenes

The late-stage biosynthetic pathway of the indole diterpene shearinine involving four enzymatic reactions (JanQDOJ) was elucidated by an efficient heterologous expression system using Aspergillus oryzae. Key oxidative cyclization, forming a characteristic A/B bicyclic shearinine core by flavoprotein oxidase, was studied using a substrate analogue and a buffer containing H₂¹⁸O. These experimental data provided evidence that JanO catalyzes two-step oxidation via a hydroxylated product and that the JanO reaction involves the hydride-transfer mechanism.

Regiospecific Prenylation of Hydroxyxanthones by a Plant Flavonoid Prenyltransferase

C-Prenylated xanthones are pharmacologically attractive specialized metabolites that are distributed in plants and microorganisms. The prenylation of xanthones often contributes to the structural diversity and biological activities of these compounds. However, efficient regiospecific prenylation of xanthones is still challenging. In this study, the regiospecific prenylation of a number of structurally different hydroxyxanthones (3-10) by MaIDT, a plant flavonoid prenyltransferase with substrate flexibility from Morus alba, is demonstrated. Among the enzymatic products, 2-dimethylallyl-1,3,7-trihydroxyxanthone (3a) effectively attenuated glutamate-induced injury in SK-N-SH neuroblastoma cells. These results suggest a potential approach for the synthesis of bioactive prenylated xanthones by a substrate-relaxed flavonoid prenyltransferase.

Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products

Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.

Saturation mutagenesis on Tyr205 of the cyclic dipeptide C2-prenyltransferase FtmPT1 results in mutants with strongly increased C3-prenylating activity

The fungal indole prenyltransferase FtmPT1 is involved in the biosynthesis of fumitremorgins and catalyzes, in the presence of dimethylallyl diphosphate, a predominant regular prenylation of cyclo-L-Trp-L-Pro (brevianamide F) at position C-2 of the indole nucleus. Analysis of the substrate-bound structure of FtmPT1 revealed that brevianamide F forms a hydrogen bond via its carbonyl oxygen in the diketopiperazine moiety with the hydroxyl group of Tyr205 near the center of the prenyltransferase (PT) barrel. In this study, Tyr205 was mutated to 19 other proteinogenic amino acids by one-step site-directed mutagenesis. The obtained mutants were assayed in the presence of dimethylallyl diphosphate with brevianamide F. The enzyme products were isolated on HPLC and their structures were elucidated by NMR and MS analyses. Mutation of Tyr205 to Phe or Met did not change the behavior of FtmPT1 significantly, with regularly C2-prenylated brevianamide F as the predominant product. Interestingly, 15 of the obtained mutants also produced regularly C3-prenylated brevianamide F, with relative yields between 33 and 110 % of those of the regularly C2-prenylated derivatives. Among them, Y205C, Y205L, Y205N, Y205I, and Y205S showed similar brevianamide F consumption. Y205H, Y205Q, Y205V, Y205G, and Y205E showed activities between 47 and 77 % of that of the wild type. These results provide a solid basis for the construction of a brevianamide F regular C3-prenyltransferase by site-directed mutagenesis. Assaying stereoisomers of brevianamide F, cyclo-D-Trp-D-Pro, cyclo-L-Trp-D-Pro, and cyclo-D-Trp-L-Pro, with two selected mutants Y205N and Y205L resulted in the formation of reversely C3-prenylated derivatives as predominant products, being in sharp contrast to their regularly C2- and C3-prenylated derivatives with cyclo-L-Trp-L-Pro.

Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases

Prenylation reactions play crucial roles in controlling the activities of biomolecules. Bacterial prenyltransferases, TleC from Streptomyces blastmyceticus and MpnD from Marinactinospora thermotolerans, catalyse the ‘reverse' prenylation of (−)-indolactam V at the C-7 position of the indole ring with geranyl pyrophosphate or dimethylallyl pyrophosphate, to produce lyngbyatoxin or pendolmycin, respectively. Using in vitro analyses, here we show that both TleC and MpnD exhibit relaxed substrate specificities and accept various chain lengths (C₅–C₂₅) of the prenyl donors. Comparisons of the crystal structures and their ternary complexes with (−)-indolactam V and dimethylallyl S-thiophosphate revealed the intimate structural details of the enzyme-catalysed ‘reverse' prenylation reactions and identified the active-site residues governing the selection of the substrates. Furthermore, structure-based enzyme engineering successfully altered the preference for the prenyl chain length of the substrates, as well as the regio- and stereo-selectivities of the prenylation reactions, to produce a series of unnatural novel indolactams.

Regioselective prenylation of small aromatic natural molecules is crucial for their biological activity. Here, the authors present the biochemical and structural characterisation of two prenyltransferases and a structure-based engineering strategy to modulate their substrate specificity.

Harvesting the biosynthetic machineries that cultivate a variety of indispensable plant natural products

Plants are a sustainable resource for valuable natural chemicals best illustrated by large-scale farming centered on specific products. Here, we review recent discoveries of plant metabolic pathways producing natural products with unconventional biomolecular structures. Prenylation of polyketides by aromatic prenyltransferases (aPTases) ties together two of the major groups of plant specialized chemicals, terpenoids and polyketides, providing a core modification leading to new bioactivities and downstream metabolic processing. Moreover, PTases that biosynthesize Z-terpenoid precursors for small molecules such as lycosantalene have recently been found in the tomato family. Gaps in our understanding of how economically important compounds such as cannabinoids are produced are being identified using next-generation 'omics' to rapidly advance biochemical breakthroughs at an unprecedented rate. For instance, olivetolic acid cyclase, a polyketide synthase (PKS) co-factor from Cannabis sativa, directs the proper cyclization of a polyketide intermediate. Elucidations of spatial and temporal arrangements of biosynthetic enzymes into metabolons, such as those used to control the efficient production of natural polymers such as rubber and defensive small molecules such as linamarin and lotaustralin, provide blueprints for engineering streamlined production of plant products.

Characterisation of 6-DMATSMo from Micromonospora olivasterospora leading to identification of the divergence in enantioselectivity, regioselectivity and multiple prenylation of tryptophan prenyltransferases

Identification of a new tryptophan prenyltransferase 6-DMATS_Mo and different behaviours of DMATS enzymes for regiospecific mono- and diprenylations of l- and d-tryptophan as well as methylated derivatives.

Impacts and perspectives of prenyltransferases of the DMATS superfamily for use in biotechnology

Prenylated compounds are ubiquitously found in nature and demonstrate interesting biological and pharmacological activities. Prenyltransferases catalyze the attachment of prenyl moieties from different prenyl donors to various acceptors and contribute significantly to the structural and biological diversity of natural products. In the last decade, significant progress has been achieved for the prenyltransferases of the dimethylallyltryptophan synthase (DMATS) superfamily. More than 40 members of these soluble enzymes are identified in microorganisms and characterized biochemically. These enzymes were also successfully used for production of a large number of prenylated derivatives. N1-, C4-, C5-, C6-, and C7-prenylated tryptophan and N1-, C2-, C3-, C4-, and C7-prenylated tryptophan-containing peptides were obtained by using DMATS enzymes as biocatalysts. Tyrosine and xanthone prenyltransferases were used for production of prenylated derivatives of their analogs. More interestingly, the members of the DMATS superfamily demonstrated intriguing substrate and catalytic promiscuity and also used structurally quite different compounds as prenyl acceptors. Prenylated hydroxynaphthalenes, flavonoids, indolocarbazoles, and acylphloroglucinols, which are typical bacterial or plant metabolites, were produced by using several fungal DMATS enzymes. Furthermore, the potential usage of these enzymes was further expanded by using natural or unnatural DMAPP analogs as well as by coexpression with other genes like NRPS and by development of whole cell biocatalyst.