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At least 829 records · Page 46Linked to original sources
PubMed1988

Molecular organisation of the quinic acid utilization (QUT) gene cluster in Aspergillus nidulans.

The functional integrity of the QUTB gene (encoding quinate dehydrogenase) has been confirmed by transformation of a qutB mutant strain. The DNA sequence of the contiguous genes QUTD (quinate permease), QUTB and QUTG (function unknown) has been determined and analysed, together with that of QUTE (catabolic 3-dehydroquinase). The QUTB sequence shows significant homology with the shikimate dehydrogenase function of the complex AROM locus of Aspergillus nidulans, and with the QA-3 quinate dehydrogenase and QA-1S (repressor) genes of Neurospora crassa. The QUTD gene shows strong homology with the N. crassa QA-Y gene and QUTG with the QA-X gene. QUTD, QUTB, and QUTG, QUTE form two pairs of divergently transcribed genes, and conserved sequence motifs identified in the two common 5' non-coding regions show significant homology with UASGAL and UASQA sequences of the Saccharomyces cerevisiae and N. crassa Gal and QA systems. In addition, conserved 5' sequences homologous to the mammalian CAAT box are noted and a previously unreported conserved 22 nucleotide motif is presented.

Alcohol Oxidoreductases↗
PubMed1990

A cDNA encoding 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Solanum tuberosum L.

A cDNA encoding potato (Solanum tuberosum L.) 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, the first enzyme of the shikimate pathway, was cloned into phage lambda gt11. The clone represents the first cDNA for this enzyme from any eukaryotic source. The nucleotide sequence of the cDNA was determined, and its identity was confirmed through partial amino acid sequence analysis of the encoded enzyme. The cDNA contains a 1527-base pair open reading frame that encodes a polypeptide with a calculated molecular weight of 56,153. The amino terminus of the deduced polypeptide resembles a chloroplast transit sequence. Amino acid sequence identities between the mature potato enzyme and the homologous isoenzymes from Escherichia coli are only about 22%. The potato cDNA hybridized to various plant mRNAs that are all about 2 kilobases in size.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed2001

Interaction of the herbicide glyphosate with its target enzyme 5-enolpyruvylshikimate 3-phosphate synthase in atomic detail.

Biosynthesis of aromatic amino acids in plants, many bacteria, and microbes relies on the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, a prime target for drugs and herbicides. We have identified the interaction of EPSP synthase with one of its two substrates (shikimate 3-phosphate) and with the widely used herbicide glyphosate by x-ray crystallography. The two-domain enzyme closes on ligand binding, thereby forming the active site in the interdomain cleft. Glyphosate appears to occupy the binding site of the second substrate of EPSP synthase (phosphoenol pyruvate), mimicking an intermediate state of the ternary enzyme.substrates complex. The elucidation of the active site of EPSP synthase and especially of the binding pattern of glyphosate provides a valuable roadmap for engineering new herbicides and herbicide-resistant crops, as well as new antibiotic and antiparasitic drugs.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed1988

Structure, expression, and evolution of the 5-enolpyruvylshikimate-3-phosphate synthase genes of petunia and tomato.

5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase is an enzyme of the shikimate pathway which is located in the chloroplasts in higher plants. This enzyme is the target of the nonselective herbicide glyphosate. We have isolated and sequenced cDNA clones encoding EPSP synthase from petunia and tomato. The deduced amino acid sequences of the two enzyme precursors show 93% identity in the mature protein regions and 58% identity in the transit peptides. The sequences of the plant enzymes show significantly greater similarity to bacterial EPSP synthases than to fungal EPSP synthases. A genomic clone containing an EPSP synthase gene was isolated from a library of petunia DNA and was shown to contain seven intervening sequences. This gene is expressed approximately 25-fold higher in flower petals than in other organs of petunia. Transcription of this gene is initiated at multiple sites in petunia leaves and in a glyphosate-tolerant petunia cell line overproducing EPSP synthase mRNA. In petals, however, transcription of this gene is initiated almost entirely from only one of these sites. In contrast to petunia, the levels of EPSP synthase mRNA in different organs of tomato do not differ significantly.

3-Phosphoshikimate 1-Carboxyvinyltransferase↗
PubMed1997

Fractionation of glycoside precursors of aroma in grapes and wine.

The glycosides in mono-, di- and trihydroxylated terpene and norisoprenoid alcohols and also those in the related shikimate pathway have been isolated on C18 reversed-phase cartridges and then fractionated into classes of different polarity at increasing percentages of methanol. The benzyl alcohol glycosides are the most polar, while those of terpene monohydroxylated alcohols and geranic acid are the least polar. The terpene diols, linalool furanoid and pyranoid oxides and also norisoprenoid precursors show intermediate polarity and separate into well defined fractions according to their polarity.

Butadienes↗
PubMed2003

Wavelength-dependent induction of a mycosporine-like amino acid in a rice-field cyanobacterium, Nostoc commune: role of inhibitors and salt stress.

Wavelength-dependent induction of a mycosporine-like amino acid (MAA) was studied in a nitrogen-fixing rice-field cyanobacterium, Nostoc commune. HPLC studies showed the presence of shinorine, a bisubstituted MAA containing both glycine and serine groups and having an absorption maximum at 334 nm. Exposure of cultures to simulated solar radiation in combination with various cut-off filters (WG 280, 295, 305, 320, 335, 345, GG 400, 420, 455, 475, OG 515, 530, 570, RG 645, 665; all Schott filter series) clearly indicated that MAAs were induced by UV-B radiation, while UV-A and PAR had very little effect on MAA induction in this organism. The ratio of the absorption at 334 nm (shinorine) to 665 nm (chlorophyll a) and the derived action spectrum also revealed the induction of MAAs to be UV-B dependent with a prominent peak at 290 nm and a second small peak at 310 nm. Various concentrations (50-300 mM) of NaCl were used to test whether another common stress factor, such as osmotic stress, also induces MAAs, as has been reported for other cyanobacterial species. The results indicate that cells grown at high concentration of NaCl but without UV-B did not show any MAA induction. In order to elucidate the possible photoreceptors, the effects of various inhibitors/quenchers on the induction of MAAs were studied. There was a marked reduction in the amount of MAA when the cells were irradiated with UV-B in the presence of inhibitors of the shikimate pathway (glyphosate, 1 mM), photosynthesis [3-(3,4-dichlorophenyl)-1,1-dimethylurea, 20 microM], protein synthesis (chloramphenicol, 25 microg ml(-1)), pterin synthesis (N-acetylserotonin, 5 mM, and 2,4-diamino-6-hydroxypyrimidine, 5 mM) and a quencher of the excited state of flavins and pterins (phenylacetic acid, 1 mM).

Amino Acids↗
PubMed1985

Elicitor induction of a microsomal 5-O-(4-coumaroyl)shikimate 3'-hydroxylase in parsley cell suspension cultures.

Microsomal preparations from parsley cell suspension cultures challenged with an elicitor from Phytophthora megasperma f.sp. glycinea (Pmg) catalyze the formation of trans-5-O-caffeoylshikimate from trans-5-O-(4-coumaroyl)shikimate. Neither the cis isomer nor free 4-coumarate, 4-coumaroyl-CoA, or 5-O-(4-coumaroyl)quinate are substrates for this enzyme. The reaction is strictly dependent on NADPH as a reducing cofactor and on molecular oxygen. NADH, ascorbic acid, and 6,7-dimethyl-5,6,7,8-tetrahydropterine cannot substitute for NADPH. However, NADH enhances enzyme activity observed in the presence of NADPH. Cytochrome c and carbon monoxide inhibit the hydroxylation reaction, suggesting a cytochrome P-450-dependent mixed-function monooxygenase.

Caffeine↗
PubMed2006

Role of glutamate 243 in the active site of 2-deoxy-scyllo-inosose synthase from Bacillus circulans.

2-Deoxy-scyllo-inosose (DOI) synthase is involved in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics and catalyzes the carbocyclic formation from d-glucose-6-phosphate (G-6-P) into DOI. The reaction mechanism is proposed to be similar to that of dehydroquinate (DHQ) synthase in the shikimate pathway, and includes oxidation of C-4, beta-elimination of phosphate, reduction of C-4, ring opening, and intramolecular aldol cyclization. To investigate the reaction mechanism of DOI synthase, site-directed mutational analysis of three presumable catalytically important amino acids of DOI synthase derived from the butirosin producer Bacillus circulans (BtrC) was carried out. Steady state and pre-steady state kinetic analysis suggested that E243 of BtrC is catalytically involved in the phosphate elimination step. Further analysis of the mutant E243Q of BtrC using substrate analogue, glucose-6-phosphonate, clearly confirmed that E243 was responsible to abstract a proton at C-5 in G-6-P and set off phosphate elimination. This glutamate residue is completely conserved in all DOI synthases identified so far and the corresponding amino acid of DHQ synthase is completely conserved as asparagine. Therefore, this characteristic glutamate residue of DOI synthase is a key determinant to distinguish the reaction mechanism between DOI synthase and DHQ synthase as well as primary sequence.

Amino Acid Sequence↗
PubMed2003

Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae.

Chorismate synthase (EC 4.2.3.5), the seventh enzyme in the shikimate pathway, catalyzes the transformation of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate, which is the last common precursor in the biosynthesis of numerous aromatic compounds in bacteria, fungi, and plants. The chorismate synthase reaction involves a 1,4-trans-elimination of phosphoric acid from EPSP and has an absolute requirement for reduced FMN as a cofactor. We have determined the three-dimensional x-ray structure of the yeast chorismate synthase from selenomethionine-labeled crystals at 2.2-A resolution. The structure shows a novel betaalphabetaalpha fold consisting of an alternate tight packing of two alpha-helical and two beta-sheet layers, showing no resemblance to any documented protein structure. The molecule is arranged as a tight tetramer with D2 symmetry, in accordance with its quaternary structure in solution. Electron density is missing for 23% of the amino acids, spread over sequence regions that in the three-dimensional structure converge on the surface of the protein. Many totally conserved residues are contained within these regions, and they probably form a structured but mobile domain that closes over a cleft upon substrate binding and catalysis. This hypothesis is supported by previously published spectroscopic measurements implying that the enzyme undergoes considerable structural changes upon binding of both FMN and EPSP.

Amino Acid Sequence↗
PubMed1996

Cloning, sequencing, expression, purification and preliminary characterization of a type II dehydroquinase from Helicobacter pylori.

A heat-stable dehydroquinase was purified to near homogeneity from a plate-grown suspension of the Gram-negative stomach pathogen Helicobacter pylori, and shown from both its subunit and native molecular masses to be a member of the type II family of dehydroquinases. This was confirmed by N-terminal amino acid sequence data. The gene encoding this activity was isolated following initial identification, by random sequencing of the H. pylori genome, of a 96 bp fragment, the translated sequence of which showed strong identity to a C-terminal region of other type II enzymes. Southern blot analysis of a cosmid library identified several potential clones, one of which complemented an Escherichia coli aroD point mutant strain deficient in host dehydroquinase. The gene encoding the H. pylori type II dehydroquinase (designated aroQ) was sequenced. The translated sequence was identical to the N-terminal sequence obtained directly from the purified protein, and showed strong identity to other members of the type II family of dehydroquinases. The enzyme was readily expressed in E. coli from a plasmid construct from which several milligrams of protein could be isolated, and the molecular mass of the protein was confirmed by electrospray MS. The aroQ gene in H. pylori may function in the central biosynthetic shikimate pathway of this bacterium, thus opening the way for the construction of attenuated strains as potential vaccines as well as offering a new target for selective enzyme inhibition.

Amino Acid Sequence↗
PubMed2002

The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis.

Attempts to construct Mycobacterium tuberculosis strains with a defect in the common aromatic amino acid biosynthesis pathway were made. In other bacteria the genes of this pathway (aro) can be disrupted in the presence of suitable media supplements. The genomic organization of the aro genes in M. tuberculosis reveals that there is one operon (aroCKBQ) and three isolated aro genes (aroE, aroG and aroA). The aroK gene was chosen as a target for disruption; this encodes shikimate kinase, which catalyses the fifth step in chorismate biosynthesis. Attempts to replace the wild-type aroK gene with a disrupted allele (aroKDelta::hyg) by a two-step homologous recombination procedure were unsuccessful in a wild-type strain. When a second functional copy of aroK was integrated into the chromosome, it was possible to isolate a strain carrying the disrupted gene. Excision of the L5-integrated copy of aroK by the L5 excisionase could be not be achieved in the strain carrying the disrupted copy, but was possible in a strain carrying a wild-type copy. These results demonstrate that the chorismate pathway is essential for the viability of M. tuberculosis.

Amino Acids, Aromatic↗
PubMed2003

Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.

Shikimate dehydrogenase catalyzes the fourth step of the shikimate pathway, the essential route for the biosynthesis of aromatic compounds in plants and microorganisms. Absent in metazoans, this pathway is an attractive target for nontoxic herbicides and drugs. Escherichia coli expresses two shikimate dehydrogenase paralogs, the NADP-specific AroE and a putative enzyme YdiB. Here we characterize YdiB as a dual specificity quinate/shikimate dehydrogenase that utilizes either NAD or NADP as a cofactor. Structures of AroE and YdiB with bound cofactors were determined at 1.5 and 2.5 A resolution, respectively. Both enzymes display a similar architecture with two alpha/beta domains separated by a wide cleft. Comparison of their dinucleotide-binding domains reveals the molecular basis for cofactor specificity. Independent molecules display conformational flexibility suggesting that a switch between open and closed conformations occurs upon substrate binding. Sequence analysis and structural comparison led us to propose the catalytic machinery and a model for 3-dehydroshikimate recognition. Furthermore, we discuss the evolutionary and metabolic implications of the presence of two shikimate dehydrogenases in E. coli and other organisms.

Adenosine↗
PubMed1998

Expression of bacterial chorismate pyruvate-lyase in tobacco: evidence for the presence of chorismate in the plant cytosol.

The bacterial gene ubiC encodes chorismate pyruvate-lyase, an enzyme which converts chorismate to 4-hydroxybenzoate and which is not normally present in plants. The UbiC protein was expressed in tobacco, with targeting of the gene product either to the plastids or to the cytosol. In both cases, chorismate pyruvate-lyase activity and a resulting formation of 4-hydroxybenzoate was detected. This suggests that chorismate, a metabolite of the shikimate pathway, is present not only in the plastids but also in the cytosol of plant cells.

Agrobacterium tumefaciens↗
PubMed2026

Genome-scale overexpression screening identifies product tolerance and efflux transport as key determinants of high-level L-tryptophan production in Escherichia coli.

L-tryptophan is a high-value aromatic amino acid widely used in the food, feed, and pharmaceutical industries. However, large-scale microbial production is constrained by insufficient precursor supply and limited strain tolerance to high product concentrations. In this study, modular metabolic engineering was first employed to enhance the availability of key precursors, including shikimate, serine, and glutamine, yielding strain TRPJ-13 with a 34.6% increase in L-tryptophan titer. To enhance strain tolerance, an indigo-based high-throughput reporter system was constructed and coupled with genome-scale overexpression library screening, leading to the identification of soxS as a tolerance-conferring target. Mechanistic analysis demonstrated that soxS upregulated lpxC to enhance lipopolysaccharide biosynthesis, thereby reinforcing membrane integrity and improving L-tryptophan tolerance. Combinatorial engineering of soxS and lpxC generated strain TRPJ-23, which increased L-tryptophan tolerance by 74.8% and L-tryptophan titer by 10.3%. Furthermore, YicL was identified as a novel transmembrane protein involved in L-tryptophan transport that effectively promoted L-tryptophan efflux, further increasing the titer by 9.0%. After fermentation optimization, strain TRPJ-28 produced 74.3 g/L L-tryptophan in a 5-L bioreactor, with a yield of 0.26 g/g and a productivity of 1.24 g/L/h. In a 1000-L pilot-scale bioreactor, TRPJ-28 reached a titer, yield, and productivity of 70.4 g/L, 0.25 g/g, and 1.17 g/L/h, respectively. This study provides new engineering insights for developing industrially promising L-tryptophan-producing strains.

Genome-scale overexpression screening↗
PubMed1986

Glyphosate inhibits photosynthesis and allocation of carbon to starch in sugar beet leaves.

Application of glyphosate (N-[phosphonomethyl] glycine) to exporting leaves of sugar beet (Beta vulgaris, L.) during the day lowered stomatal conductance and carbon fixation. Allocation of newly fixed carbon to foliar starch accumulation was nearly completely inhibited, being decreased by the same amount as net carbon fixation. In contrast, decreasing net carbon fixation in untreated leaves by lowering CO(2) concentration caused starch accumulation to decrease, but only in the same proportion as net carbon fixation. Shikimate level increased 50-fold in treated leaves but the elevated rate of carbon accumulation in shikimate was only 4% of the decrease in the rate of starch accumulation. Application of steady state labeling with (14)CO(2) to exporting leaves confirmed the above changes in carbon metabolism, but revealed no other major daytime differences in the (14)C-content of amino acids or other compounds between treated and control leaves. Less (14)C accumulated in treated leaves because of decreased fixation, not increased export. The proportion of newly fixed carbon allocated to sucrose increased, maintaining export at the level in control leaves. Returning net carbon exchange to the rate before treatment restored starch accumulation fully and prevented a decrease in export during the subsequent dark period.

Journal Article↗
PubMed2001

Pigment and virulence deficiencies associated with mutations in the aroE gene of Xanthomonas oryzae pv. oryzae.

Xanthomonadins are yellow, membrane-bound pigments produced by members of the genus Xanthomonas. We identified an ethyl methanesulfonate-induced Xanthomonas oryzae pv. oryzae mutant (BXO65) that is deficient for xanthomonadin production and virulence on rice, as well as auxotrophic for aromatic amino acids (Pig(-) Vir(-) Aro(-)). Reversion analysis indicated that these multiple phenotypes are due to a single mutation. A genomic library of the wild-type strain was used to isolate a 7.0-kb clone that complements BXO65. By transposon mutagenesis, marker exchange, sequence analysis, and subcloning, the complementing activity was localized to a 849-bp open reading frame (ORF). This ORF is homologous to the aroE gene, which encodes shikimate dehydrogenase in various bacterial species. Shikimate dehydrogenase activity was present in the wild-type strain and the mutant with the complementing clone, whereas no activity was found in BXO65. This clone also complemented an Escherichia coli aroE mutant for prototrophy, indicating that aroE is functionally conserved in X. oryzae pv. oryzae and E. coli. The nucleotide sequence of the 2.9-kb region containing aroE revealed that a putative DNA helicase gene is located adjacent to aroE. Our results indicate that aroE is required for normal levels of virulence and xanthomonadin production in X. oryzae pv. oryzae.

Alcohol Oxidoreductases↗
PubMed2001

A small decrease of plastid transketolase activity in antisense tobacco transformants has dramatic effects on photosynthesis and phenylpropanoid metabolism.

Transketolase (TK) catalyzes reactions in the Calvin cycle and the oxidative pentose phosphate pathway (OPPP) and produces erythrose-4-phosphate, which is a precursor for the shikimate pathway leading to phenylpropanoid metabolism. To investigate the consequences of decreased TK expression for primary and secondary metabolism, we transformed tobacco with a construct containing an antisense TK sequence. The results were as follows: (1) a 20 to 40% reduction of TK activity inhibited ribulose-1,5-bisphosphate regeneration and photosynthesis. The inhibition of photosynthesis became greater as irradiance increased across the range experienced in growth conditions (170 to 700 micromol m(-2) sec(-1)). TK almost completely limited the maximum rate of photosynthesis in saturating light and saturating CO(2). (2) Decreased expression of TK led to a preferential decrease of sugars, whereas starch remained high until photosynthesis was strongly inhibited. One of the substrates of TK (fructose-6-phosphate) is the starting point for starch synthesis, and one of the products (erythrose-4-phosphate) inhibits phosphoglucose isomerase, which catalyzes the first reaction leading to starch. (3) A 20 to 50% decrease of TK activity led to decreased levels of aromatic amino acids and decreased levels of the intermediates (caffeic acid and hydroxycinnamic acids) and products (chlorogenic acid, tocopherol, and lignin) of phenylpropanoid metabolism. (4) There was local loss of chlorophyll and carotene on the midrib when TK activity was inhibited by >50%, spreading onto minor veins and lamina in severely affected transformants. (5) OPPP activity was not strongly inhibited by decreased TK activity. These results identify TK activity as an important determinant of photosynthetic and phenylpropanoid metabolism and show that the provision of precursors by primary metabolism colimits flux into the shikimate pathway and phenylpropanoid metabolism.

Antisense Elements (Genetics)↗
PubMed2002

Maize pollen enzymes after two-dimensional polyacrylamide gel electrophoresis in the presence or absence of sodium dodecyl sulfate.

Twelve enzymes from mature pollen grains of maize were separated by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The separation in the second dimension was both in the presence and absence of sodium dodecyl sulfate (SDS). Ten of the investigated enzymes lost activity after separation in the presence of SDS, but those of esterases and acid phosphatase could be recovered. On the other hand, 2-D electrophoresis without SDS is suitable for the analysis of maize pollen pectinesterase, malate dehydrogenase, glutamic-oxalacetic transaminase, diaphorase, superoxide dismutase, and phosphoglucose isomerase. 1-D PAGE and isoelectric focusing (IEF) are sufficient to analyze glucose-6-phosphate dehydrogenase, alcohol dehydrogenase, shikimic dehydrogenase, and glutamate dehydrogenase. The possibility of applying 2-D electrophoresis for the analysis of enzymes from single stigma and stigma exudate is dicussed.

Electrophoresis, Gel, Two-Dimensional↗