Biosynthesis of Violacein: Origins of Hydrogen,Nitrogen and Oxygen Atoms in the 2-Pyrrolidone Nucleus

The biosynthetic origins of the hydrogen, nitrogen and oxygen atoms in the pyrrolidone ring of violacein'were established by an anaylses of the ¹H, ¹³C NMR and MS spectra of its isotope-enriched metabolites. Feeding experiments of [2-²H] and [3-²H₂]tryptophans have revealed that the hydrogen in the pyrrolidone ring was derived from the methylene protons at the 3-position of tryptophan. The stereochemical fate of the prochiral hydrogens was determined to be in the retention of the pro-S hydrogen by these feeding experiments using [3R-²H] and [3S”-²H]tryptophans. The incorporation experiment of [α-¹⁵N]tryptophan demonstrated that the nitrogen atom in the ring originated from the α-amino group of tryptophan. The incorporation experiment of ¹⁸O₂ gas verified that all the oxygen atoms of violacein were derived from the molecular oxygen.     

Violacein and related tryptophan metabolites produced by <Emphasis Type="Italic">Chromobacterium violaceum</Emphasis>: biosynthetic mechanism and pathway for construction of violacein core

Violacein is a natural violet pigment produced by several Gram-negative bacteria, including Chromobacterium violaceum, Janthinobacterium lividum, and Pseudoalteromonas tunicata D2, among others. This pigment has potential medical applications as antibacterial, anti-trypanocidal, anti-ulcerogenic, and anticancer drugs. The structure of violacein consists of three units: a 5-hydroxyindole, an oxindole, and a 2-pyrrolidone. The biosynthetic origins of hydrogen, nitrogen, and carbon in the pyrrolidone nucleus were established by feeding experiments using various stable isotopically labeled tryptophans (Trps). Pro-S hydrogen of CH₂ at the 3-position of Trp is retained during biosynthesis. The nitrogen atom is exclusively from the α-amino group, and the skeletal carbon atoms originate from the side chains of the two Trp molecules. All three oxygen atoms in the violacein core are derived from molecular oxygen. The most interesting biosynthetic mechanism is the 1,2-shift of the indole nucleus on the left side of the violacein scaffold. The alternative Trp molecule is directly incorporated into the right side of the violacein core. This indole shift has been observed only in violacein biosynthesis, despite the large number of natural products having been isolated. There were remarkable advances in biosynthetic studies in 2006–2008. During the 3 years, most of the intermediates and the complete pathway were established. Two independent processes are involved: the enzymatic process catalyzed by the five proteins VioABCDE or the alternative nonenzymatic oxidative decarboxylation reactions. The X-ray crystallographic structure of VioE that mediates the indole rearrangement reaction was recently identified, and the mechanism of the indole shift is discussed here.     

Environments and conformations of tryptophan side chains of gramicidin A in phospholipid bilayers studied by Raman spectroscopy.

Raman spectroscopy has been used to investigate the hydrophobic interaction of the indole ring with the environments, the water accessibility to the N1H site, and the conformation about the C beta-C3 bond for the four tryptophan side chains of gramicidin A incorporated into phospholipid bilayers. Most of the tryptophan side chains of the head-to-head helical dimer transmembrane channel are strongly interacting with the lipid hydrocarbon chains, and the hydrophobic interactions for the rest increase with increasing hydrocarbon chain length of the lipid. One tryptophan side chain (probably Trp-15) is accessible to water molecules, another (Trp-9) is deeply buried in the bilayer and inaccessible, and the accessibilities of the remaining two (Trp-11 and Trp-13) depend on the bilayer thickness. The torsional angle about the C beta-C3 bond is found to be +/- 90 degrees for all the tryptophans irrespective of the membrane thickness. Binding of the sodium cation to the channel does not change the torsional angles but decreases the water accessibilities of two tryptophans (Trp-11 and Trp-13) considerably. In conjunction with a slight spectral change in the amide III region, it is suggested that the sodium binding causes a partial change in the main-chain conformation around Trp-11 and Trp-13, which results in the movements of these side chains toward the bilayer center. Two models consistent with the present Raman data are proposed for the tryptophan orientation in the dominant channel structure.     

Tryptophan interactions in bacteriorhodopsin: a heteronuclear solid-state NMR study

The bulky and amphiphilic nature of tryptophan residues makes them particularly interesting components of proteins. In bacteriorhodopsin, four of the eight tryptophan residues are in the active site, forming parts of the retinal binding pocket. In this work, we use solid-state NMR to study the interactions of the tryptophan residues in wild-type bacteriorhodopsin, in the resting state, and in critical intermediates of the proton-motive photocycle. The range of the chemical shifts of the indole nitrogens suggests that all eight of them are hydrogen bonded. Using difference spectroscopy, we isolate several changes in these hydrogen bonds in the early and late M states. As found earlier for the peptide backbone, some perturbations found in the early M state relax in the transition to the late M state while new perturbations arise. Interestingly, Rotational Echo DOuble Resonance (REDOR) difference spectroscopy of [20-13C]retinal,[indole-15N]Trp-bR shows that indole of Trp182 is not involved in the significant hydrogen bond perturbations. We also use REDOR to measure dipolar interactions in [20-13C]retinal,[indole-15N]Trp-bR, and thereby determine the distance between the C20 of retinal and the indole nitrogen of Trp182. The internuclear distance changes only slightly from the light-adapted state (3.36 +/- 0.2 A) to the early M state (3.16 +/- 0.4 A).     

The role of tryptophan as a biosynthetic precursor of indole-diterpenoid fungal metabolites: Continuing a debate

Studies in the 1980s and 1990s on the origin of the indole moiety in fungal indole-diterpenoids using ¹⁴C-labelled tryptophan consistently showed autoradiographic evidence but gave low % incorporation of the probe. Recent studies on a member of the group (nodulisporic acid A), using more specific ¹³C methodology, demonstrated a role of the tryptophan biosynthetic pathway but, in failing to show involvement of end-product, concluded that the indole was derived from indole-3-glycerol phosphate and suggested that the previous ¹⁴C data arose via metabolic scrambling of label. In considering the protocol for the ¹³C studies, there is concern that the fungal material was starved of an exogenous nitrogen source and thus could have degraded added labelled tryptophan. Consequently, synthesis of the serine necessary for anabolic formation of tryptophan may have been constrained. It is suggested that ¹³C studies on appropriate fungi early in the idiophase of submerged or surface fermentation should be made before the biosynthesis of indole-diterpenoids can become clearer.     

Incorporation of Label from 13C-, 2H-, and 15N-Labeled Methionine Molecules during the Biosynthesis of 2[prime]-Deoxymugineic Acid in Roots of Wheat

The biosynthetic pathway of 2[prime]-deoxymugineic acid, a key phytosiderophore, was investigated by feeding 13C-, 2H-, and 15N-labeled methionine, the first precursor, to the roots of hydroponically cultured wheat (Triticum aestivum L. cv Minori). The incorporation of label from each methionine species was observed during their conversion to 2[prime]-deoxymugineic acid, using 2H-, 15N-, and 13C-nuclear magnetic resonance (NMR). L-[1-13C]Methionine (99% 13C) was efficiently incorporated, resulting in 13C enrichment of the three carboxyl groups of 2[prime]-deoxymugineic acid. Use of D,L-[15N]methionine (95% 15N) resulted in 15N enrichment of 2[prime]-deoxymugineic acid at the azetidine ring nitrogen and the secondary amino nitrogen. When D,L-[2,3,3,-2H3-S-methyl-2H3]methionine (98.2% 2H) was fed to the roots, 2H-NMR results indicated that only six deuterium atoms were incorporated, and that the deuterium atom from the C-2 position of each methionine was almost completely lost. [2,2,3,3-2H4]1-Aminocyclopropane-1-carboxylic acid (98% 2H) was not incorporated into 2[prime]-deoxymugineic acid. These data and our previous findings demonstrated that only the deuterium atom from the C-2 position of L-methionine was lost, and that other atoms were completely incorporated when three molecules of methionine were converted to 2[prime]-deoxymugineic acid. These observations are consistent with the conversion of L-methionine to azetidine-2-carboxylic acid, suggesting that L-methionine is first converted to azetidine-2-carboxylic acid during biosynthesis leading to 2[prime]-deoxymugineic acid. Based on these results, a hypothetical pathway from L-methionine to 2[prime]-deoxymugineic acid was postulated.     

A study on the tricarboxylic acid cycle and the synthesis of acetylcholine in the lobster nerve

1. The biosynthetic origin of the amide substituent of N-(alpha-hydroxyethyl)lysergamide has been studied. 2. [1-(14)C]Acetate, [(14)C]formate, [2-(14)C]mevalonic acid lactone, [2-(14)C]indole, dl-[3-(14)C]tryptophan, dl-[3-(14)C]serine, dl-[2-(14)C]alanine and [2-(14)C]pyruvate were efficiently incorporated into the alkaloid, but not dl-[1-(14)C]alanine or [1-(14)C]pyruvate. 3. Only the dl-[2-(14)C]alanine- and [2-(14)C]pyruvate-derived alkaloid contained appreciable radioactivity in the amide substituent. 4. l-[(15)N]Alanine-derived alkaloid was shown to be specifically labelled in the amide nitrogen. However, l-[(14)C,(15)N]alanine was found to be incorporated into the methylcarbinolamide substituent with an appreciable increase in the (15)N/(14)C ratio, suggesting that alanine is not the direct precursor of this moiety.     

Biosynthesis of a trypanocide by Chromobacterium violaceum

Radio-isotope studies indicated not only that l-tryptophan can serve as carbon source for synthesis of the trypanocide, violacein by Chromobacterium violaceum (BB-78 strain) but also that isatin and indole 3-acetic acid are both important metabolic intermediates. Using 3-indolyl [2-¹⁴C] and [1-¹⁴C] acetic acid, it was found that the carboxylic carbon was not eliminated and that indole-3-acetic acid was incorporated intact into the pigment structure. N-Ethyl(5-hydroxy-indol-3-yl)-2-indolylethylamide is also an important metabolic intermediate in the violacein biosynthesis. This is the first report of a metabolic scheme for violacein synthesis which includes an intermediate other than l-tryptophan.     

Biosynthesis of camptothecin. In silico and in vivo tracer study from [1-13C]glucose

Camptothecin derivatives are clinically used antitumor alkaloids that belong to monoterpenoid indole alkaloids. In this study, we investigated the biosynthetic pathway of camptothecin from [1-13C]glucose (Glc) by in silico and in vivo studies. The in silico study measured the incorporation of Glc into alkaloids using the Atomic Reconstruction of Metabolism software and predicted the labeling patterns of successive metabolites from [1-13C]Glc. The in vivo study followed incorporation of [1-13C]Glc into camptothecin with hairy roots of Ophiorrhiza pumila by 13C nuclear magnetic resonance spectroscopy. The 13C-labeling pattern of camptothecin isolated from the hairy roots clearly showed that the monoterpene-secologanin moiety was synthesized via the 2C-methyl-D-erythritol 4-phosphate pathway, not via the mevalonate pathway. This conclusion was supported by differential inhibition of camptothecin accumulation by the pathway-specific inhibitors (fosmidomycin and lovastatin). The quinoline moiety from tryptophan was also labeled as predicted by the Atomic Reconstruction of Metabolism program via the shikimate pathway. These results indicate that camptothecin is formed by the combination of the 2C-methyl-D-erythritol 4-phosphate pathway and the shikimate pathway. This study provides the innovative example for how a computer-aided comprehensive metabolic analysis will refine the experimental design to obtain more precise biological information.     

Biosynthesis of bisorbicillinoid in Trichoderma sp. USF-2690; evidence for the biosynthetic pathway,via sorbicillinol,of sorbicillin,bisorbicillinol, bisorbibutenolide,and bisorbicillinolide

An incorporation study of [1-(13)C] and [1,2-(13)C2] labeled sodium acetates into sorbicillinol 1 established a ring closure system between C-1 and C-6 and the positions that were oxidized and/or methylated on a hexaketide chain. Subsequent investigations, using 13C-labeled 1 prepared from [1-(13)C] labeled sodium acetate, clearly demonstrated that both bisorbicillinol 2 and sorbicillin 6 incorporated 13C-labeled 1 into their carbon skeletons. 13C-labeled bisorbicillinols 2 derived from [1-(13)C]- and [2-(13)C]-labeled sodium acetates clearly indicate that these were on the biosynthetic route from 1 to bisorbibutenolide (bislongiquinolide) 3 and bisorbicillinolide 4 via 2 as a branching point in the fungus.     

Biosynthetic origin of graphenone in cultured lichen mycobionts of Graphis handelii

The biosynthetic origins of the carbon skeleton in graphenone were verified by feeding the culture of spore-derived mycobionts of the lichen Graphis handelii with sodium [1-13C]-acetate, sodium [1,2-13C2]-acetate, sodium [2-13C]-pyruvate, [1,2,3-13C]-glycerol, [13CH3]-methionine and sodium [1,4-13C2]-succinate.     

Production of a novel tryptophan analog, beta-1-indazole-L-alanine with tryptophan synthase of Escherichia coli

The tryptophan synthase alpha 2 beta 2 complex from Escherichia coli has been found to catalyze the beta-replacement reaction of L-serine with indazole, an indole analog which has a nitrogen atom at the 2-position (pyrazole ring). The reaction product was isolated and identified as beta-indazolealanine by mass spectrometric, elemental and NMR analyses. Careful assignment of 1H- and 13C-signals with several NMR techniques revealed that the beta-carbon of the product alanine moiety was bound to the 1-N-position of the indazole ring. This is the first example of the beta-replacement reaction catalyzed by tryptophan synthase occurring at any other position than the 3-position of indole analogs.     

The membrane interface dictates different anchor roles for "inner pair" and "outer pair" tryptophan indole rings in gramicidin A channels

We investigated the effects of substituting two of the four tryptophans (the "inner pair" Trp(9) and Trp(11) or the "outer pair" Trp(13) and Trp(15)) in gramicidin A (gA) channels. The conformational preferences of the doubly substituted gA analogues were assessed using circular dichroism spectroscopy and size-exclusion chromatography, which show that the inner tryptophans 9 and 11 are critical for the gA's conformational preference in lipid bilayer membranes. [Phe(13,15)]gA largely retains the single-stranded helical channel structure, whereas [Phe(9,11)]gA exists primarily as double-stranded conformers. Within this context, the (2)H NMR spectra from labeled tryptophans were used to examine the changes in average indole ring orientations, induced by the Phe substitutions and by the shift in conformational preference. Using a method for deuterium labeling of already synthesized gAs, we introduced deuterium selectively onto positions C2 and C5 of the remaining tryptophan indole rings in the substituted gA analogues for solid-state (2)H NMR spectroscopy. The (least possible) changes in orientation and overall motion of each indole ring were estimated from the experimental spectra. Regardless of the mixture of backbone folds, the indole ring orientations observed in the analogues are similar to those found previously for gA channels. Both Phe-substituted analogues form single-stranded channels, as judged from the formation of heterodimeric channels with the native gA. [Phe(13,15)]gA channels have Na(+) currents that are ~50% and lifetimes that are ~80% of those of native gA channels. The double-stranded conformer(s) of [Phe(9,11)]gA do not form detectable channels. The minor single-stranded population of [Phe(9,11)]gA forms channels with Na(+) currents that are ~25% and single-channel lifetimes that are ~300% of those of native gA channels. Our results suggest that Trp(9) and Trp(11), when "reaching" for the interface, tend to drive both monomer folding (to "open" a channel) and dimer dissociation (to "close" a channel). Furthermore, the dipoles of Trp(9) and Trp(11) are relatively more important for the single-channel conductance than are the dipoles of Trp(13) and Trp(15).     

Biosynthesis of thiamine. Incorporation experiments with 14C-labelled substrates and with [15N]glycine in Saccharomyces cerevisiae

1. Yeast was grown in a minimal synthetic medium together with a range of (14)C-labelled substrates under standardized conditions. After isolation, the purified thiamine was cleaved by sulphite and the pyrimidine and thiazole moieties were purified and assayed for radioactivity. 2. In order of decreasing incorporation, [(14)C]formate, [3-(14)C]serine, [2-(14)C]glycine and [2-(14)C]acetate supplied label for the pyrimidine, and [2-(14)C]glycine, [3-(14)C]serine, [1-(14)C]glycine, [(14)C]formate and [2-(14)C]acetate for the thiazole. Incorporation of label into the fragments from several other (14)C-labelled substrates, including [Me-(14)C]- and [3,4-(14)C(2)]-methionine, was insignificant. 3. [3-(14)C]Serine was shown not to contribute label to C-2 of the thiazole ring. 4. Significant incorporation of nitrogen from [(15)N]glycine into the thiazole moiety, but not into the pyrimidine moiety, was established. 5. It appears that C-2 and N-3 of the thiazole ring are formed from C-2 and the nitrogen atom of glycine, but the entire methionine molecule does not appear to be implicated.     

Natural and directed biosynthesis of communesin alkaloids

A role for tryptophan, acetate, mevalonate and methionine in the biosynthesis of communesins A and B, novel structurally-related and biologically-active Penicillium metabolites, has been established by isotopic labelling techniques. The incorporation of (14)C-tryptamine has also been demonstrated. dl-2-(13)C-tryptophan specifically enriched two carbon atoms in the (13)C NMR spectrum, thereby defining the intra-molecular arrangement of the two tryptophan-derived moieties. Feeding differentially labelled precursors during communesin production showed that tryptophan and methionine are involved early in the biosynthesis and that mevalonate provides an isoprene which is added later. A biosynthetic pathway involving an early precursor based on tryptophan is proposed. Indole-N-((13)C-methyl) tryptophan was not incorporated into communesins implying that N-methylation of tryptophan is not the first step of the communesin biosynthetic pathway. During deamination of indole-N-((13)C-methyl) tryptophan to 1-(13)C-methylindole-3-carboxylic acid communesin biosynthesis was inhibited. Of several halogenated indoles tested for directed biosynthesis, only dl-6-fluoro-tryptophan and 6-fluoro-tryptamine caused accumulation of the corresponding monofluoro-analogues of communesins A and B.     

Tryptophan perturbation in the L intermediate of bacteriorhodopsin: fourier transform infrared analysis with indole-15N shift.

In the photoreaction of bacteriorhodopsin, the L intermediate shows an intense band at 3486 cm-1 which is unaffected by 2H2O (Maeda, A., Sasaki, J., Shichida, Y., & Yoshizawa, T. (1992) Biochemistry 31, 462-467]. This band is shifted to 3477 cm-1 by [indole-15N]tryptophan substitution and therefore is assigned to the N-H stretching vibration of the indole of tryptophan. Free indole in carbon tetrachloride shows its N-H stretching vibration at 3491 cm-1 [Fuson, N., Josien, M.-L., Powell, R. L., & Utterback, E. (1952) J. Chem. Phys. 20, 145-152]. Thus, it is suggested that at least one tryptophan residue in the L intermediate is not hydrogen bonded.     

13C NMR study of the biosynthesis of toxins by Fusarium graminearum

13C NMR spectroscopic investigations on the biosynthesis of mycotoxins produced by Fusarium graminearum (M69) were carried out through the incorporation of [1-13C]- and [2-13C]acetate precursors. The major secondary metabolites produced by this species in still culture were deoxynivalenol (3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-one), 15-acetyldeoxynivalenol, zearalenone, and butenolide. [1-13C]- and [2-13C]acetate were incorporated in alternate carbon atoms in zearalenone, consistent with the head to tail condensation of nine acetate units. The trichothecenes were enriched in a manner consistent with the condensation of three mevalonate units. 13C/13C couplings, observed between C-5 and C-12, as well as between C-6 and C-15 of 15-acetyldeoxynivalenol, confirms the current hypothesis of formation of the trichothecene ring system by cyclization of farnesyl pyrophosphate. The incorporation pattern in ergosterol is also consistent with a mevalonate origin, while the adjacent incorporation of acetate methyl groups in butenolide suggests a glutamate precursor. The degree of enrichment in the secondary metabolites, which ranged from 3 to 10% at each carbon site, was observed in the 13C NMR spectra of the crude fungal extracts to be dependent on the timing of acetate addition to the culture. The specific toxins produced together with the quantity of each, were also found to be dependent on the timing of acetate addition. Competition between the three biosynthetic pathways of secondary metabolism, i.e. polyketide, mevalonate, and amino acid for the labeled acetate in this organism is a complex function of culture conditions.     

A Novel Metabolic Pathway for Indole-3-Acetic Acid in Apical Shoots of Populus tremula (L.) x Populus tremuloides (Michx.)

Metabolism of indole-3-acetic acid (IAA) in apical shoots of Populus tremula (L.) x Populus tremuloides (Michx.) was investigated by feeding a mixture of [12C]IAA, [13C6]IAA, and [1[prime]-14C]IAA through the base of the excised stem. HPLC of methanolic plant extracts revealed eight major radiolabeled metabolites after a 24-h incubation period. Comparison between feeds with [5-3H]IAA and [1[prime]-14C]IAA showed that all detectable metabolites were nondecarboxylative products. The purified radiolabeled HPLC fractions were screened by frit-fast atom bombardment liquid chromatography-mass spectrometry for compounds with characteristic fragment pairs originating from the application with 12C and 13C isotopes. Samples of interest were further characterized by gas chromatography-mass spectrometry. Using this procedure, oxindole-3-acetic acid (OxIAA), indole-3-acetyl-N-aspartic acid (IAAsp), oxindole-3-acetyl-N-aspartic acid (OxIAAsp), and ring-hydroxylated oxindole-3-acetic acid were all identified as IAA metabolites. Furthermore, a novel metabolic pathway from IAA via IAAsp and OxIAAsp to OxIAA was established on the basis of refeeding experiments with the different IAA metabolites.     

Biosynthesis of the 3-benzylchroman-4-one eucomin in Eucomis bicolor

Feeding experiments have demonstrated the specific incorporation of radioactivity from dl-phenylalanine-[1-¹⁴C], l-phenylalanine-[U-¹⁴C], sodium acetate-[2-¹⁴C] and l-methionine-[methyl-¹⁴C] into the 3-benzylchroman-4-one eucomin in Eucomis bicolor. The labelling patterns indicate that eucomin is biosynthesized by the addition of a carbon atom derived from methionine onto a C₁₅ chalcone-type skeleton. Radioactivity from 2′,4′,4-trihydroxy-6′-methoxychalcone-[methyl-¹⁴C] and 2′,4′-dihydroxy-4,6′-dimethoxychalcone-[6′-methyl-¹⁴C] was incorporated into eucomin, the latter compound being the better precursor, demonstrating the feasibility that 2′-methoxychalcones are biosynthetic precursors of the “homoisoflavonoids”. Possible biosynthetic relationships in this class of compounds are discussed.     

Biosynthetic studies on the tropane ring system of the tropane alkaloids from Datura stramonium

Isotopic labelling experiments have been carried out in Datura stramonium root cultures with the following isotopically labelled precursors; [2H3]- [2-13C, 2H3]-, [1-13C, 18O2]-acetates, 2H2O, [2H3-methyl]-methionine, [2-13C]-phenyllactate, [3-2H]-tropine and [2'-13C, 3-2H]-littorine. The study explored the incorporation of isotope into the tropane ring system of littorine 1 and hyoscyamine 2 and revealed that deuterium from acetate is incorporated only into C-6 and C-7, and not into C-2 and C-4 as previously reported. Oxygen-18 was not retained at a detectable level into the C(3)-O bond from [1-13C, 18O2]-acetate. The intramolecular nature of the rearrangement of littorine 1 to hyoscyamine 2 is revealed again by a labelling study using [2'-13C, 3-2H]-littorine, [2-13C]-phenyllactate and [3-2H]-tropine.