Crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana provides insights into its product specificity

Flavor precursors identification and thermal degradation mechanisms of glucoerucin in fragrant rapeseed oil

The degradation products of glucosinolates endow rapeseed oil with a characteristic aroma, however, the mechanism remains unclear. In this study, 29 individual glucosinolates were identified in six rapeseeds (Brassica napus) using widely targeted metabolism, including 22 aliphatic, 5 aromatic, and 2 indole glucosinolates. Characterization of thermally induced aromas from new precursors-glucoerucin was performed in different pH matrices via headspace-solid phase microextraction and gas chromatography-mass spectrometry. Six glucoerucin degradation were identified including 5-methylthio-pentanenitrile and dimethyl trisulfide et al. The results of thermal model showed that Glucoerucin could generate volatile 5-methylthio-pentanenitrile via dehydration and formed 1-isothiocyanato-4-(methylsulfanyl)butane via (394.9 μg/kg) by the Rosen rearrangement further product pungent odors 4-isothiocyanato-1-butene (5.6 μg/kg) at pH 5. Sulfur-containing compounds included dimethyl disulfide and dimethyl trisulfide can provide pungent and cabbage notes in matrices at pH 7 and 9. The results provide a new understanding in the forming mechanism of characteristic odor in fragrant rapeseed oil.

Characterization of the active site in the thiocyanate-forming protein from Thlaspi arvense (TaTFP) using EPR spectroscopy

Glucosinolates are plant thioglucosides, which act as chemical defenses. Upon tissue damage, their myrosinase-catalyzed hydrolysis yields aglucones that rearrange to toxic isothiocyanates. Specifier proteins such as thiocyanate-forming protein from Thlaspi arvense (TaTFP) are non-heme iron proteins, which capture the aglucone to form alternative products, e.g. nitriles or thiocyanates. To resolve the electronic state of the bound iron cofactor in TaTFP, we applied continuous wave electron paramagnetic resonance (CW EPR) spectroscopy at X-and Q-band frequencies (∼9.4 and ∼34 GHz). We found characteristic features of high spin and low spin states of a d 5 electronic configuration and local rhombic symmetry during catalysis. We monitored the oxidation states of bound iron during conversion of allylglucosinolate by myrosinase and TaTFP in presence and absence of supplemented Fe2+. Without added Fe2+, most high spin features of bound Fe3+ were preserved, while different g'-values of the low spin part indicated slight rearrangements in the coordination sphere and/or structural geometry. We also examined involvement of the redox pair Fe3+/Fe2 in samples with supplemented Fe2+. The absence of any EPR signal related to Fe3+ or Fe2+ using an iron-binding deficient TaTFP variant allowed us to conclude that recorded EPR signals originated from the bound iron cofactor.

Lifetimes of the Aglycone Substrates of Specifier Proteins, the Autonomous Iron Enzymes That Dictate the Products of the Glucosinolate-Myrosinase Defense System in Brassica Plants

Specifier proteins (SPs) are components of the glucosinolate-myrosinase defense system found in plants of the order Brassicales (brassicas). Glucosinolates (GLSs) comprise at least 150 known S-(β-d-glucopyranosyl)thiohydroximate-O-sulfonate compounds, each with a distinguishing side chain linked to the central carbon. Following tissue injury, the enzyme myrosinase (MYR) promiscuously hydrolyzes the common thioglycosidic linkage of GLSs to produce unstable aglycone intermediates, which can readily undergo a Lossen-like rearrangement to the corresponding organoisothiocyanates. The known SPs share a common protein architecture but redirect the breakdown of aglycones to different stable products: epithionitrile (ESP), nitrile (NSP), or thiocyanate (TFP). The different effects of these products on brassica consumers motivate efforts to understand the defense response in chemical detail. Experimental analysis of SP mechanisms is challenged by the instability of the aglycones and would be facilitated by knowledge of their lifetimes. We developed a spectrophotometric method that we used to monitor the rearrangement reactions of the MYR-generated aglycones from nine GLSs, discovering that their half-lives (t_1/2) vary by a factor of more than 50, from <3 to 150 s (22 °C). The t_1/2 of the sinigrin-derived allyl aglycone (34 s), which can form the epithionitrile product (1-cyano-2,3-epithiopropane) in the presence of ESP, proved to be sufficient to enable spatial and temporal separation of the MYR and ESP reactions. The results confirm recent proposals that ESP is an autonomous iron-dependent enzyme that intercepts the unstable aglycone rather than a direct effector of MYR. Knowledge of aglycone lifetimes will enable elucidation of how the various SPs reroute aglycones to different products.

Molecular Modeling of Epithiospecifier and Nitrile-Specifier Proteins of Broccoli and Their Interaction with Aglycones

Glucosinolates are secondary plant metabolites of Brassicaceae. They exert their effect after enzymatic hydrolysis to yield aglycones, which become nitriles and epithionitriles through the action of epithiospecifier (ESP) and nitrile-specifier proteins (NSP). The mechanism of action of broccoli ESP and NSP is poorly understood mainly because ESP and NSP structures have not been completely characterized and because aglycones are unstable, thus hindering experimental measurements. The aim of this work was to investigate the interaction of broccoli ESP and NSP with the aglycones derived from broccoli glucosinolates using molecular simulations. The three-dimensional structure of broccoli ESP was built based on its amino-acid sequence, and the NSP structure was constructed based on a consensus amino-acid sequence. The models obtained using Iterative Threading ASSEmbly Refinement (I-TASSER) were refined with the OPLS-AA/L all atom force field of GROMACS 5.0.7 and were validated by Veryfy3D and ERRAT. The structures were selected based on molecular dynamics simulations. Interactions between the proteins and aglycones were simulated with Autodock Vina at different pH. It was concluded that pH determines the stability of the complexes and that the aglycone derived from glucoraphanin has the highest affinity to both ESP and NSP. This agrees with the fact that glucoraphanin is the most abundant glucosinolate in broccoli florets.

Glucosinolate structural diversity, identification, chemical synthesis and metabolism in plants

The glucosinolates (GSLs) is a well-defined group of plant metabolites characterized by having an S-β-d-glucopyrano unit anomerically connected to an O-sulfated (Z)-thiohydroximate function. After enzymatic hydrolysis, the sulfated aglucone can undergo rearrangement to an isothiocyanate, or form a nitrile or other products. The number of GSLs known from plants, satisfactorily characterized by modern spectroscopic methods (NMR and MS) by mid-2018, is 88. In addition, a group of partially characterized structures with highly variable evidence counts for approximately a further 49. This means that the total number of characterized GSLs from plants is somewhere between 88 and 137. The diversity of GSLs in plants is critically reviewed here, resulting in significant discrepancies with previous reviews. In general, the well-characterized GSLs show resemblance to C-skeletons of the amino acids Ala, Val, Leu, Trp, Ile, Phe/Tyr and Met, or to homologs of Ile, Phe/Tyr or Met. Insufficiently characterized, still hypothetic GSLs include straight-chain alkyl GSLs and chain-elongated GSLs derived from Leu. Additional reports (since 2011) of insufficiently characterized GSLs are reviewed. Usually the crucial missing information is correctly interpreted NMR, which is the most effective tool for GSL identification. Hence, modern use of NMR for GSL identification is also reviewed and exemplified. Apart from isolation, GSLs may be obtained by organic synthesis, allowing isotopically labeled GSLs and any kind of side chain. Enzymatic turnover of GSLs in plants depends on a considerable number of enzymes and other protein factors and furthermore depends on GSL structure. Identification of GSLs must be presented transparently and live up to standard requirements in natural product chemistry. Unfortunately, many recent reports fail in these respects, including reports based on chromatography hyphenated to MS. In particular, the possibility of isomers and isobaric structures is frequently ignored. Recent reports are re-evaluated and interpreted as evidence of the existence of "isoGSLs", i.e. non-GSL isomers of GSLs in plants. For GSL analysis, also with MS-detection, we stress the importance of using authentic standards.

Structural diversification during glucosinolate breakdown: mechanisms of thiocyanate, epithionitrile and simple nitrile formation

Secondary metabolism is characterized by an impressive structural diversity. Here, we have addressed the mechanisms underlying structural diversification upon damage-induced activation of glucosinolates, a group of thioglucosides found in the Brassicales. The classical pathway of glucosinolate activation involves myrosinase-catalyzed hydrolysis and rearrangement of the aglucone to an isothiocyanate. Plants of the Brassicaceae possess specifier proteins, i.e. non-heme iron proteins that promote the formation of alternative products by interfering with this reaction through unknown mechanisms. We have used structural information available for the thiocyanate-forming protein from Thlaspi arvense (TaTFP), to test the impact of loops protruding at one side of its β-propeller structure on product formation using the allylglucosinolate aglucone as substrate. In silico loop structure sampling and semiempirical quantum mechanical calculations identified a 3L2 loop conformation that enabled the Fe2+ cofactor to interact with the double bond of the allyl side chain. Only this arrangement enabled the formation of allylthiocyanate, a specific product of TaTFP. Simulation of 3,4-epithiobutane nitrile formation, the second known product of TaTFP, required an alternative substrate docking arrangement in which Fe2+ interacts with the aglucone thiolate. In agreement with these results, substitution of 3L2 amino acid residues involved in the conformational change as well as exchange of critical amino acid residues of neighboring loops affected the allylthiocyanate versus epithionitrile proportion obtained upon myrosinase-catalyzed allylglucosinolate hydrolysis in the presence of TaTFP in vitro. Based on these insights, we propose that specifier proteins are catalysts that might be classified as Fe2+ -dependent lyases.

Identification Of N-Acetyl-S-(3-Cyano-2-(Methylsulfanyl)Propyl-Cysteine as a Major Human Urine Metabolite from the Epithionitrile 1-Cyano-2,3-Epithiopropane, the Main Glucosinolate Hydrolysis Product from Cabbage

Brassica vegetables such as cabbage or pak choi contain alkenyl glucosinolates which can release epithionitriles and to a lesser degree isothiocyanates upon enzymatic hydrolysis. Here, for the first time, the metabolism of an epithionitrile was investigated in humans, namely 1-cyano-2,3-epithiopropane (CETP). After consumption of Brassica oleracea var. capitata f. alba and Brassica carinata sprouts, the main urinary metabolite of CETP was identified as N-acetyl-S-(3-cyano-2-(methylsulfanyl)propyl-cysteine using an UHPLC-ESI-QToF-MS approach and synthesis of the metabolite. This urinary epithionitrile metabolite is an S-methylated mercapturic acid. No other metabolites were detected. Then, in a preliminary pilot experiment the excretion kinetics of CETP were investigated in three volunteers. After consumption of a B. carinata sprout preparation containing 50.8 µmol of CETP, urinary N-acetyl-S-(3-cyano-2-(methylsulfanyl)propyl-cysteine concentrations were the highest three hours after consumption, ranging from 23.9 to 37.2 µM, and declined thereafter. Thus, epithionitriles are bioavailable compounds that are metabolized similarly to isothiocyanates by the mercapturic acid pathway. In the future, more epithionitrile metabolites should be identified and the pharmacokinetics of these important class of dietary compounds should be assessed in more detail.

Iron is a centrally bound cofactor of specifier proteins involved in glucosinolate breakdown

Glucosinolates, a group of sulfur-rich thioglucosides found in plants of the order Brassicales, have attracted a lot of interest as chemical defenses of plants and health promoting substances in human diet. They are accumulated separately from their hydrolyzing enzymes, myrosinases, within the intact plant, but undergo myrosinase-catalyzed hydrolysis upon tissue disruption. This results in various biologically active products, e.g. isothiocyanates, simple nitriles, epithionitriles, and organic thiocyanates. While formation of isothiocyanates proceeds by a spontaneous rearrangement of the glucosinolate aglucone, aglucone conversion to the other products involves specifier proteins under physiological conditions. Specifier proteins appear to act with high specificity, but their exact roles and the structural bases of their specificity are presently unknown. Previous research identified the motif EXXXDXXXH as potential iron binding site required for activity, but crystal structures of recombinant specifier proteins lacked the iron cofactor. Here, we provide experimental evidence for the presence of iron (most likely Fe²⁺) in purified recombinant thiocyanate-forming protein from Thlaspi arvense (TaTFP) using a Ferene S-based photometric assay as well as Inductively Coupled Plasma-Mass Spectrometry. Iron binding and activity depend on E266, D270, and H274 suggesting a direct interaction of Fe²⁺ with these residues. Furthermore, we demonstrate presence of iron in epithiospecifier protein and nitrile-specifier protein 3 from Arabidopsis thaliana (AtESP and AtNSP3). We also present a homology model of AtNSP3. In agreement with this model, iron binding and activity of AtNSP3 depend on E386, D390, and H394. The homology model further suggests that the active site of AtNSP3 imposes fewer restrictions to the glucosinolate aglucone conformation than that of TaTFP and AtESP due to its larger size. This may explain why AtNSP3 does not support epithionitrile or thiocyanate formation, which likely requires exact positioning of the aglucone thiolate relative to the side chain.

Differences in the enzymatic hydrolysis of glucosinolates increase the defense metabolite diversity in 19 Arabidopsis thaliana accessions

Plants of the order Brassicales produce glucosinolates (GS), a group of secondary metabolites that are part of an elaborate defense system. But it is not the GS itself rather its enzymatic hydrolysis products that cause the bioactive effects protecting the plants against pests and pathogens. Thus the enzymatic hydrolysis and a variety of additional influential factors determine the structural outcome of the GS degradation process. To evaluate the possible diversity of defense metabolites a range of 19 Arabidopsis thaliana accessions were selected showing divergence in their geographical origin, in their phenotype, and in their GS profile. These particular accessions accumulate several alkenyl GS, hydroxyalkyl GS, methylthioalkyl GS, and methylsulfinylalkyl GS in their rosette leaves whereas the indole GS contents are relatively invariant, as analyzed by UHPLC-DAD. After tissue disruption the enzymatic formation of GS hydrolysis products was examined and breakdown products were identified and quantified by GC-MS. Great differences in the amount and structure of volatile enzymatic degradation products could be observed in the different accessions, with strong variation in formation of epithionitriles, nitriles, and isothiocyanates. The occurrence of specific GS hydrolysis products was put in relation to relative gene expression profiles of myrosinases and specifier proteins as measured by RT-qPCR, and in relation to relative protein abundance of epithiospecifier protein. Dependent on the different GS profiles and reliant on degradation protein abundance and composition the ecotypes strongly varied in their ability to form isothiocyanates, nitriles and epithionitriles, thus increasing the plants' equipment of defense metabolites.

Crystal structure of the nitrile-specifier protein NSP1 from Arabidopsis thaliana

As important components of the glucosinolate-myrosinase system, specifier proteins mediate plant defense against herbivory and pathogen attacks. After tissue disruption, glucosinolates are hydrolyzed by myrosinases to instable aglucones, which will rearrange to form defensive isothiocyanates. Nevertheless, this reaction could be redirected to form other products by specifier proteins. Up to now, identified specifier proteins include epithiospecifier proteins (ESPs), thiocyanate forming proteins (TFPs), and nitrile-specifier proteins (NSPs). Recently, the structures of ESP and TFP have been reported. However, both the structure and the catalytic mechanism of NSPs remain enigmatic. Here, we solved the crystal structure of the NSP1 protein from Arabidopsis thaliana (AtNSP1). Structural comparisons with ESP and TFP proteins revealed several structural features of AtNSP1 different from those of the two proteins. Subsequent molecular docking studies showed that the R292 residue in AtNSP1 displayed a conformation different from those of the corresponding residues in ESP and TFP proteins, which might account for the product specificity and catalytic mechanism of AtNSP1. Taken together, the present study provides important insights into the molecular mechanisms underlying the different product spectrums between NSPs and the other two types of specifier proteins, and shed light on the future studies of the detailed mechanisms of other specifier proteins.