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Biosynthesis of isochorismate in Klebsiella pneumoniae: origin of O-2.

The shikimate metabolites are key precursors to a large number of natural products, including aromatic amino acids. Chorismic acid is an important branch point in the biosynthetic pathway to aromatic amino acids. Chorismic acid is also unique among natural products since it is the only compound known to undergo an enzymatic Claisen rearrangement. A metabolite of chorismic acid, isochorismic acid, first observed in Aerobacter aerogenes differs in its chemical structure by the location of the hydroxyl group and the double bonds. Isochorismic acid is a precursor to a growing number of shikimate-derived metabolites. Isochorismic acid has also been postulated to be an intermediate of m-carboxyaromatic amino acids, implying another enzymatic Claisen rearrangement. In this publication, we have isolated isochorismate synthase and found that on lyophilization the enzyme is stable for at least 6 months at -20 degrees C. Incubation of chorismate with this preparation in water enriched with 18O led to incorporation of one atom of 18O as proven from the fast atom bombardment mass spectra of the HPLC purified derived isochorismate.

Chorismic Acid↗

[Intramolecular isotope distribution of metabolites in the glycolytic chain].

Based on the mechanism of the fractionation of carbon isotopes in the glycolytic chain proposed earlier, a method for the qualitative prediction of intramolecular isotope distribution of metabolites synthesized through the glycolytic chain and conjugated reactions was developed. Among them are fatty acids, monoterpenes, hopanoids, branched amino acids, amino acids of the family of trioses, metabolites synthesized by the shikimate pathway, metabolites of the Krebs cycle, amino acids of the family of ketoglutaric and oxalacetic acids. The method was tested by comparing the natural and theoretically predicted isotope distributions of carbon. The model for the description of theoretical isotope distributions is based on oscillations in the glycolytic chain. In the glycolysis phase, an isotope effect of decarboxylation of pyruvate arises, which determines the experimentally observed isotope inhomogeneity of metabolites. The isotope distributions of carbon depend on the sequence of syntheses of metabolites in the cell cycle, which corresponds to the degrees of exhaustion of the pyruvate depot that supplies structural units for the synthesis. In repeated cycles, the syntheses of metabolites occur in phase in addition to the carbon flux passing through the glycolytic chain, a carbon flux entering from the photorespiratory chain is involved in the synt, which is enriched in carbon heavy isotope. This flux is used, in particular, for the formation of carbon fragments of complex molecules.

Amino Acids, Branched-Chain↗

Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine.

Francisella tularensis is the etiological agent of tularemia, a serious disease in several Northern hemisphere countries. The organism has fastidious growth requirements and is very poorly understood at the genetic and molecular levels. Given the lack of data on this organism, we undertook the sample sequencing of its genome. A random library of DNA fragments from a highly virulent strain (Schu 4) of F. tularensis was constructed and the nucleotide sequences of 13,904 cloned fragments were determined and assembled into 353 contigs. A total of 1.83 Mb of nucleotide sequence was obtained that had a G+C content of 33.2%. Genes located on plasmids pOM1 and pNFL10, which had been previously isolated from low virulence strains of F. tularensis, were absent but all of the other known F. tularensis genes were represented in the assembled data. F. tularensis Schu4 was able to grow in the absence of aromatic amino acids and orthologues of genes which could encode enzymes in the shikimate pathway in other bacteria were identified in the assembled data. Genes that could encode all of the enzymes in the purine biosynthetic and most of the en- zymes in the purine salvage pathways were also identified. This data will be used to develop defined rationally attenuated mutants of F. tularensis, which could be used as replacements for the existing genetically undefined live vaccine strain.

Bacterial Vaccines↗

Sugars and Organic Acids of Vitis vinifera.

Glucose, fructose, galactose, sucrose, maltose, melibiose, raffinose, and stachyose were identified in the leaves, bark, roots, and berries of Vitis vinifera L. var. Thompson Seedless. In addition to these sugars, verbascose and manninotriose were found in the leaves and bark.Malic, tartaric, citric, isocitric, ascorbic, cis-aconitic, oxalic, glycolic, glyoxylic, succinic, lactic, glutaric, fumaric, pyrrolidone carboxylic, alpha-ketoglutaric, pyruvic, oxaloacetic, galacturonic, glucuronic, shikimic, quinic, chlorogenic, and caffeic acids were identified in the leaves, bark, roots, and berries.Glucose, fructose, sucrose, malate, tartrate, and citrate were determined quantitatively in the leaf, petiole, xylem, bark, tendril, bud, puduncle pedicel, berry, lateral roots, and main roots at 4 separate physiological stages of growth. In addition, changes in the concentrations of fructose, glucose, malate, and tartrate in leaves were measured during a 36-day period starting from budburst.

Journal Article↗

The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction.

The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most unusual since they are unrelated at the sequence level and they utilize completely different mechanisms to catalyze the same overall reaction. The type I enzymes catalyze a cis-dehydration of 3-dehydroquinate via a covalent imine intermediate, while the type II enzymes catalyze a trans-dehydration via an enolate intermediate. Here we report the three-dimensional structures of a representative member of each type of biosynthetic DHQase. Both enzymes function as part of the shikimate pathway, which is essential in microorganisms and plants for the biosynthesis of aromatic compounds including folate, ubiquinone and the aromatic amino acids. An explanation for the presence of two different enzymes catalyzing the same reaction is presented. The absence of the shikimate pathway in animals makes it an attractive target for antimicrobial agents. The availability of these two structures opens the way for the design of highly specific enzyme inhibitors with potential importance as selective therapeutic agents.

Binding Sites↗

Interference of L-alpha-aminooxy-beta-phenylpropionic acid with phenylalanine metabolism in buckwheat.

L-alpha-Aminooxy-beta-phenylpropionic acid (AOPP), a potent competitive inhibitor of phenylalanine ammonia-lyase (PAL), blocked light-induced phenylpropanoid synthesis in excised buckwheat hypocotyls and produced an up to 40-fold increase in the endogenous phenylalanine concentration, while the level of all other amino acids was hardly affected. After a 24 h incubation in the light in the presence of 0.3 or 1 mM AOPP phenylalanine alone constituted about 25% of the total soluble amino acids, compared to appr. 1% in the controls. In the presence of AOPP illuminated hypocotyls accumulated nearly 3 times more phenylalanine than hypocotyls kept in the dark, indicating an enhancing effect of light on the flow of carbon through the shikimate pathway. Exogenously added [14C]phenylalanine was extensively metabolized by control tissue, but accumulated in AOPP treated tissue. In the presence of AOPP radioactivity from [14C]shikimate accumulated predominantly in phenylalanine, and the flow of shikimate into tyrosine and phenylalanine was not affected by the inhibitor. Therefore, under these conditions no feedback control of phenylalanine and tyrosine synthesis from shikimate is apparent in buckwheat hypocotyls.

Amino Acids↗

Genetic engineering of shikonin biosynthesis hairy root cultures of Lithospermum erythrorhizon transformed with the bacterial ubiC gene.

The biosynthetic pathway to 4-hydroxybenzoate (4HB), a precursor of the naphthoquinone pigment shikonin, was modified in Lithospermum erythrorhizon hairy root cultures by introduction of the bacterial gene ubiC. This gene of Escherichia coli encodes chorismate pyruvate-lyase (CPL), an enzyme that converts chorismate into 4HB and is not normally present in plants. The ubiC gene was fused to the sequence for a chloroplast transit peptide and placed under control of a constitutive plant promoter. This construct was introduced into L. erythrorhizon by Agrobacterium rhizogenes-mediated transformation. The resulting hairy root cultures showed high CPL activity. 4HB produced by the CPL reaction was utilized for shikonin biosynthesis, as shown by in vivo inhibition of the native pathway to 4HB with 2-aminoindan-2-phosphonic acid (AIP), an inhibitor of phenylalanine ammonia-lyase. A feeding experiment with [1,7-13C2]shikimate showed that in the absence of AIP the artificially introduced CPL reaction contributed ca. 20% of the overall 4HB biosynthesis in the transgenic cultures. ubiC transformation did not lead to a statistically significant increase of shikonin formation, but to a 5-fold increase of the accumulation of menisdaurin, a nitrile glucoside which is presumably related to aromatic amino acid metabolism.

Cell Line, Transformed↗

CYP98A3 from Arabidopsis thaliana is a 3'-hydroxylase of phenolic esters, a missing link in the phenylpropanoid pathway.

The 4- and 5-hydroxylations of phenolic compounds in plants are catalyzed by cytochrome P450 enzymes. The 3-hydroxylation step leading to the formation of caffeic acid from p-coumaric acid remained elusive, however, alternatively described as a phenol oxidase, a dioxygenase, or a P450 enzyme, with no decisive evidence for the involvement of any in the reaction in planta. In this study, we show that the gene encoding CYP98A3, which was the best possible P450 candidate for a 3-hydroxylase in the Arabidopsis genome, is highly expressed in inflorescence stems and wounded tissues. Recombinant CYP98A3 expressed in yeast did not metabolize free p-coumaric acid or its glucose or CoA esters, p-coumaraldehyde, or p-coumaryl alcohol, but very actively converted the 5-O-shikimate and 5-O-d-quinate esters of trans-p-coumaric acid into the corresponding caffeic acid conjugates. The shikimate ester was converted four times faster than the quinate derivative. Antibodies directed against recombinant CYP98A3 specifically revealed differentiating vascular tissues in stem and root. Taken together, these data show that CYP98A3 catalyzes the synthesis of chlorogenic acid and very likely also the 3-hydroxylation of lignin monomers. This hydroxylation occurs on depsides, the function of which was so far not understood, revealing an additional and unexpected level of networking in lignin biosynthesis.

Arabidopsis↗

The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase.

We present here the 2.3-A crystal structure of the Escherichia coli YdiB protein, an orthologue of shikimate 5-dehydrogenase. This enzyme catalyzes the reduction of 3-dehydroshikimate to shikimate as part of the shikimate pathway, which is absent in mammals but required for the de novo synthesis of aromatic amino acids, quinones, and folate in many other organisms. In this context, the shikimate pathway has been promoted as a target for the development of antimicrobial agents. The crystal structure of YdiB shows that the protomer contains two alpha/beta domains connected by two alpha-helices, with the N-terminal domain being novel and the C-terminal domain being a Rossmann fold. The NAD+ cofactor, which co-purified with the enzyme, is bound to the Rossmann domain in an elongated fashion with the nicotinamide ring in the pro-R conformation. Its binding site contains several unusual features, including a cysteine residue in close apposition to the nicotinamide ring and a clamp over the ribose of the adenosine moiety formed by phenylalanine and lysine residues. The structure explains the specificity for NAD versus NADP in different members of the shikimate dehydrogenase family on the basis of variations in the amino acid identity of several other residues in the vicinity of this ribose group. A cavity lined by residues that are 100% conserved among all shikimate dehydrogenases is found between the two domains of YdiB, in close proximity to the hydride acceptor site on the nicotinamide ring. Shikimate was modeled into this site in a geometry such that all of its heteroatoms form high quality hydrogen bonds with these invariant residues. Their strong conservation in all orthologues supports the possibility of developing broad spectrum inhibitors of this enzyme. The nature and disposition of the active site residues suggest a novel reaction mechanism in which an aspartate acts as the general acid/base catalyst during the hydride transfer reaction.

Alcohol Oxidoreductases↗

Comparative action of glyphosate as a trigger of energy drain in eubacteria.

Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa, each possessing a 5-enolpyruvylshikimate 3-phosphate synthase that is sensitive to inhibition by glyphosate [N-(phosphonomethyl)glycine], provide a good cross-section of organisms exemplifying the biochemical diversity of the aromatic pathway targeted by this potent antimicrobial compound. The pattern of growth inhibition, the alteration in levels of aromatic-pathway enzymes, and the accumulation of early-pathway metabolites after the addition of glyphosate were distinctive for each organism. Substantial intracellular shikimate-3-phosphate accumulated in response to glyphosate treatment in all three organisms. Both E. coli and P. aeruginosa, but not B. subtilis, accumulated near-millimolar levels of shikimate-3-phosphate in the culture medium. Intracellular backup of common-pathway precursors of shikimate-3-phosphate was substantial in B. subtilis, moderate in P. aeruginosa, and not detectable in E. coli. The full complement of aromatic amino acids prevented growth inhibition and metabolite accumulation in E. coli and P. aeruginosa where amino acid end products directly control early-pathway enzyme activity. In contrast, the initial prevention of growth inhibition in the presence of aromatic amino acids in B. subtilis was succeeded by progressively greater growth inhibition that correlated with rapid metabolite accumulation. In B. subtilis glyphosate can decrease prephenate concentrations sufficiently to uncouple the sequentially acting loops of feedback inhibition that ordinarily link end product excess to feedback inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase by prephenate. The consequential unrestrained entry is an energy-rich substrates into the aromatic pathway, even in the presence of aromatic amino acid end products, is an energy drain that potentially accounts for the inability of end products to fully reverse glyphosate inhibition in B. subtilis. Even in E. coli after glyphosate inhibition and metabolite accumulation were allowed to become fully established, a transient period where end products were capable of only partial reversal of growth inhibition occurred. The distinctive metabolism produced by dissimilation of different carbon sources also profound effects upon glyphosate sensitivity.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity.

The type I 3-dehydroquinate dehydratase (DHQase) which catalyses the reversible dehydration of 3-dehydroquinic acid to 3-dehydroshikimic acid is involved in the shikimate pathway for the biosynthesis of aromatic compounds. The shikimate pathway is absent in mammals, which makes structural information about DHQase vital for the rational design of antimicrobial drugs and herbicides. The crystallographic structure of the type I DHQase from Salmonella typhi has now been determined for the native form at 1.78 A resolution (R = 19.9%; R(free) = 24.7%). The structure of the modified enzyme to which the product has been covalently bound has also been determined but in a different crystal form (2.1 A resolution; R = 17.7%; R(free) = 24.5%). An analysis of the three available crystal forms has provided information about the physiological dimer interface. The enzyme relies upon the closure of a lid-like loop to complete its active site. As the lid-loop tends to stay in the closed position, dimerization appears to play a role in biasing the arrangement of the loop towards its open position, thus facilitating substrate access.

Binding Sites↗

Gene-enzyme relationships of aromatic acid biosynthesis in Bacillus subtilis.

Mutants have been isolated which correspond to every step concerned with the biosynthesis of the aromatic amino acids in Bacillus subtilis. Each mutant has been characterized, and the lesion it bore was analyzed by deoxyribonucleic acid transformation and PBS-1 mediated transduction. The biochemical analysis revealed that each of the mutations appears to have affected a single enzyme, except for two groups of pleiotropic mutations. All aroF mutants (chorismic acid synthetase) lack dehydroquinic acid synthetase (aroB) activity. The gene that specifies aroB is closely linked to the gene coding for the aroF enzyme. Both genes are a part of the aro cluster. Mutants lacking chorismate mutase activity also lack d-arabino-heptulosonic acid-7-phosphate synthetase and shikimate kinase activity, presumably as a result of these three activities forming a multi-enzyme complex. Another mutant, previously undescribed, had been isolated. The affected gene codes for the tyrosine and phenylalanine aminotransferase activity. All of the mutations have been located on the B. subtilis genome except those in the genes specifying shikimate kinase activity and tyrosine-phenylalanine aminotransferase activity.

Alcohol Oxidoreductases↗

Construction of a safe, stable, efficacious vaccine against Photobacterium damselae ssp. piscicida.

Vaccination with bacterial auxotrophs, particularly those with an interruption in the common pathway of aromatic amino-acid biosynthesis, known as the shikimate pathway, has been shown to be effective in the prevention of a variety of bacterial diseases. In order to evaluate this approach to vaccine development in the important marine pathogen Photobacterium damselae subsp. piscicida, the aroA gene of the shikimate pathway was identified from a P. damselae subsp. piscicida genomic library by complementation in an aroA mutant of Escherichia coli. The complementing plasmid was isolated and the nucleotide sequence of the P. damselae subsp. piscicida genomic insert was determined. Subsequent analysis of the DNA-sequence data demonstrated that the identified plasmid contained 3464 bp of P. damselae subsp. piscicida DNA, including the complete aroA gene. The sequence data was used to delete a 144 bp MscI fragment, and the kanamycin resistance gene (kan) from transposon Tn903 was ligated into the MscI site. This delta(aro)A::kan construct was sub-cloned into a suicide plasmid and transferred to a wild-type P. damselae subsp. piscicida by conjugation and allelic exchange. One selected mutant, LSU-P2, was confirmed phenotypically to require supplementation with aromatic metabolites for growth in minimal media, and was confirmed genotypically by PCR and DNA sequencing. Further, LSU-P2 was demonstrated to be avirulent in hybrid striped bass and to provide significant protection against disease following challenge with the wild-type strain.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

The global gene expression response of Escherichia coli to L-phenylalanine.

We investigated the global gene expression changes of Escherichia coli due to the presence of different concentrations of phenylalanine or shikimate in the growth medium. The response to 0.5 g l(-1) phenylalanine primarily reflected a perturbed aromatic amino acid metabolism, in particular due to TyrR-mediated regulation. The addition of 5g l(-1) phenylalanine reduced the growth rate by half and elicited a great number of likely indirect effects on genes regulated in response to changed pH, nitrogen or carbon availability. Consistent with the observed gene expression changes, supplementation with shikimate, tyrosine and tryptophan relieved growth inhibition by phenylalanine. In contrast to the wild-type, a tyrR disruption strain showed increased expression of pckA and of tktB in the presence of phenylalanine, but its growth was not affected by phenylalanine at the concentrations tested. The absence of growth inhibition by phenylalanine suggested that at high phenylalanine concentrations TyrR-defective strains might perform better in phenylalanine production.

Bacterial Proteins↗

A genetic approach to the biosynthesis of the rifamycin-chromophore in Nocardia mediterranei. I. Isolation and characterization of a pentose-excreting auxotrophic mutant of Nocardia mediterranei with drastically reduced rifamycin production.

The mutant under study, designated A8, is derived from a Nocardia mediterranei strain, N813, which is a high rifamycin B producer. A8 is auxotrophic for aromatic amino acids and produces much less rifamycin B than the parent. A mixture of pentoses with D (--) ribulose as the main product is accumulated in the fermentation broth of this mutant. It was shown to be affected in its transketolase activity as no formation of D-sedoheptulose -7P from pentose-phosphates could be detected in vitro using crude extracts. The only pathway so far known which is derived from D-sedoheptulose-7P is the shikimate pathway leading to aromatic amino acids and vitamins. Biochemical and genetic investigations with mutant A8, which is defective in both the biosynthesis of rifamycins and the biosynthesis of shikimate pathway products, show that the seven-carbon amino unit of the rifamycin-chromophore must be derived from an intermediate of the shikimate pathway.

Culture Media↗

Slowed enzymatic turnover allows characterization of intermediates by solid-state NMR.

EPSP (5-enolpyruvylshikimate-3-phosphate) synthase catalyzes condensation of shikimate 3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form EPSP, a precursor to the aromatic amino acids. S3P and [2-13C]POP were bound to mutant or wild type E. coli forms of the enzyme prior to lyophilization. CPMAS-echo and rotational-echo double-resonance (REDOR) NMR experiments, employing a slow catalytic EPSP synthase mutant and a long prelyophilization incubation interval, allowed our observation of the gradual formation of a strong 31P-13C coupling consistent with the well characterized tetrahedral intermediate. However, after shorter low temperature incubation intervals of substrates with mutant or wild-type enzymes, carbon CPMAS-echo NMR spectra showed the 13C label at 155 ppm, consistent with sp2 geometry of this carbon. REDOR revealed that the phosphorus of PEP was cleaved. However, phosphorus at a distance of 7.5 A was observed, due to the phosphate of a nearby bound S3P. Heating the sample allowed the reaction to progress, as shown by the diminution of the 155 ppm peak and growth of a peak at 108 ppm. The sp3 geometry implied by the 108 ppm peak strongly suggested formation of a S3P-PEP condensation product. REDOR indicated that phosphorus was still distant, but now only 6.1 (wild type) or 5.9 A (mutant) distant. We think that the early intermediates with peaks at 155 and 108 ppm are covalently bound to the enzyme. We also think that the tetrahedral intermediate that we observed was formed after product was generated.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗

Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins.

The shikimate pathway is common to the biosynthesis of the three aromatic amino acids and that of various secondary metabolites in land plants. Shikimate kinase (SK; EC 2.7.1.71) catalyzes the phosphorylation of shikimate to yield shikimate 3-phosphate. In an attempt to elucidate the functional roles of enzymes that participate in the shikimate pathway in rice (Oryza sativa), we have now identified and characterized cDNAs corresponding to three SK genes--OsSK1, OsSK2, and OsSK3--in this monocotyledenous plant. These SK cDNAs encode proteins with different NH(2)-terminal regions and with putative mature regions that share sequence similarity with other plant and microbial SK proteins. An in vitro assay of protein import into intact chloroplasts isolated from pea (Pisum sativum) seedlings revealed that the full-length forms of the three rice SK proteins are translocated into chloroplasts and processed, consistent with the assumption that the different NH(2)-terminal sequences function as chloroplast transit peptides. The processed forms of all three rice proteins synthesized in vitro manifested SK catalytic activity. Northern blot analysis revealed that the expression of OsSK1 and OsSK2 was induced in rice calli by treatment with the elicitor N-acetylchitoheptaose, and that expression of OsSK1 and OsSK3 was up-regulated specifically during the heading stage of panicle development. These results suggest that differential expression of the three rice SK genes and the accompanying changes in the production of shikimate 3-phosphate may contribute to the defense response and to panicle development in rice.

Amino Acid Sequence↗

Temporally distinct accumulation of transcripts encoding enzymes of the prechorismate pathway in elicitor-treated, cultured tomato cells.

The accumulation of phenylalanine-derived phenolic compounds is a well-known element of a plant's defense in response to pathogen attack. Phenylalanine, as well as the other two aromatic amino acids, tyrosine and tryptophan, is synthesized by way of the shikimate pathway. The first seven steps of the shikimate pathway (the prechorismate pathway) are common for the biosynthesis of all three aromatic amino acids. We have studied transcript levels of six genes--i.e., two 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase genes, one shikimate kinase gene, one 5-enolpyruvylshikimate 3-phosphate synthase gene, and two chorismate synthase genes--corresponding to four steps of the prechorismate pathway, in cultured tomato cells exposed to fungal elicitors. The abundance of transcripts specific for some of these genes increased 10- to 20-fold within 6 h after elicitor treatment, as did the abundance of phenylalanine ammonialyase-specific transcripts and the synthesis of ethylene. Interestingly, transcript accumulation occurred more rapidly for shikimate kinase than for the enzymes preceding or following it in the prechorismate pathway. Neither the inhibition of ethylene biosynthesis by aminoethoxyvinylglycine nor inhibition of phenylalanine ammonia-lyase (EC 4.3.1.5) activity by 2-aminoindan-2-phosphonic acid affected the time course or extent of transcript accumulation. Thus, the increased demand for phenylalanine in the phenylpropanoid pathway required after elicitor treatment appears to be met by increased de novo synthesis of its biosynthetic enzymes.

Journal Article↗