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PubMed2004

Proteomic analysis of carbonylated proteins in two-dimensional gel electrophoresis using avidin-fluorescein affinity staining.

A method for detecting carbonylated proteins in two-dimensional electrophoresis (2-DE) was developed using biotinylation and avidin-fluorescein isothiocyanate (FITC) affinity staining. The method was used to examine oxidatively modified proteins associated with oxidative stress. Carbonyl formation in proteins was first examined in a model system by subjecting bovine serum albumin (BSA) and ribonuclease A (RNase A) to metal-catalyzed oxidation (MCO). Carbonyl group formation was found to occur at multiple sites along with a small amount of polypeptide chain cleavage. In vivo studies were conducted in yeast cell cultures using 5 mM hydrogen peroxide to induce oxidative stress. Biotinylation of yeast protein was accomplished during extraction at 4 degrees C in a lysis buffer containing 5 mM biotin-hydrazide. Biotin-hydrazide forms a Schiff base with a carbonyl group on an oxidized protein that is subsequently reduced before electrophoresis. Proteins were separated by either 2-DE or sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Biotinylated species were detected using avidin-FITC affinity staining. Detection sensitivity with biotinylated proteins was five times higher than achieved by silver staining. The limit of detection with avidin-FITC staining approached 0.64 pmol of protein-associated carbonyls. Twenty carbonylated proteins were identified in the proteome of yeast following oxidative stress with hydrogen peroxide. Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) analysis of tryptic peptides was used to identify peptides extracted from gels. Aconitase, heat shock protein SSA1 and SSC1, pyruvate decarboxylase isozyme 1, pyruvate kinase 1, enolase 1 and 2, phosphoglycerate kinase, fructose-bisphosphate aldorase, and glyceraldehyde-3-phosphate dehydrogenase were among the major targets of oxidative stress.

Animals↗

PubMed2005

Metabolic engineering of a Lactobacillus plantarum double ldh knockout strain for enhanced ethanol production.

Lactobacillus plantarum ferments glucose through the Embden-Meyerhof-Parnas pathway: the central metabolite pyruvate is converted into lactate via lactate dehydrogenase (LDH). By substituting LDH with pyruvate decarboxylase (PDC) activity, pyruvate may be redirected toward ethanol production instead of lactic acid fermentation. A PDC gene from the Gram-positive bacterium Sarcina ventriculi (Spdc) was introduced into an LDH-deficient strain, L. plantarum TF103, in which both the ldhL and ldhD genes were inactivated. Four different fusion genes between Spdc and either the S. ventriculi promoter or three Lactococcus lactis promoters in pTRKH2 were introduced into TF103. PDC activity was detected in all four recombinant strains. The engineered strains were examined for production of ethanol and other metabolites in flask fermentations. The recombinant strains grew slightly faster than the parent TF103 and produced 90-130 mM ethanol. Although slightly more ethanol was observed, carbon flow was not significantly improved toward ethanol, suggesting that a further understanding of this organism's metabolism is necessary.

Ethanol↗

PubMed2003

Dual catalytic apparatus of the thiamin diphosphate coenzyme: acid-base via the 1',4'-iminopyrimidine tautomer along with its electrophilic role.

It was recently reported (Jordan, F.; Zhang, Z.; Sergienko, E. A. Bioorg. Chem. 2002, 30, 188-198) that addition to the E477Q active-center variant of yeast pyruvate decarboxylase of (a) pyruvate on a rapid-scan UV stopped-flow, or (b) acetaldehyde or benzoylformate on a circular dichroism (CD) instrument, generates a new band with lambda(max) near 300-310 nm. A chemical model demonstrated that the wavelength is appropriate to the 1',4'-iminopyrimidine tautomer of the 4'-aminopyrimidine ring in thiamin diphosphate. Herein, we report the formation of a new positive CD band centered at 305 nm when the Escherichia colipyruvate dehydrogenase complex first E1 subunit and its variants are exposed to phosphonolactylthiamin diphosphate, a stable analogue of the covalent adduct formed between the substrate pyruvate and the C2 atom of thiamin diphosphate. The behavior of this CD band, whether it suggests saturation of the enzyme by phosphonolactylthiamin diphosphate, or its very existence (the band is not seen with the E571A E1 variant, where E571 is hydrogen bonded to the N1' atom of the 4'-aminopyrimidine ring), as well as its position are consistent with its assignment to the 1',4'-imino thiamin diphosphate tautomer on the enzyme, chiral by virtue of its fixed V conformation. The mechanism of binding of phosphonolactylthiamin diphosphate closely resembles that of thiamin diphosphate itself.

Binding Sites↗

PubMed1996

Why Saccharomyces cerevisiae can oxidize but not decarboxylate external pyruvate.

Protoplasts of the yeast Saccharomyces cerevisiae oxidized externally added pyruvate by pyruvate oxidase system but were not able to decarboxylate it anaerobically by pyruvate decarboxylase at pH 6.4 in isotonic solutions. The decarboxylation set in hypotonic solutions in which the integrity of the plasma membrane was being impaired. Yeast cells incubated with [1-14C]pyruvate accumulated radioactivity under conditions allowing oxidation of pyruvate, but virtually no pyruvate was taken up when the oxidation had been arrested by inhibition or mutation. In view of a large difference between Km for pyruvate of pyruvate decarboxylase (30 mM) and of pyruvate oxidase (0.16 mM), the results may be accounted for by the assumption that transport of pyruvate across the yeast plasma membrane is trans-inhibited by relatively high concentrations of intracellular pyruvate. This arrangement would allow utilization of external pyruvate by the cell energy-transforming machinery and, at the same time, prevent its wastage by futile decarboxylation.

Decarboxylation↗

PubMed1997

Aerobic fermentation during tobacco pollen development.

In vegetative organs of plants, the metabolic switch from respiration to fermentation is dictated by oxygen availability. The two genes dedicated to ethanolic fermentation, pyruvate decarboxylase and alcohol dehydrogenase, are induced by oxygen deprivation and the gene products are active under oxygen stress. In pollen, these two genes are expressed in a stage-specific manner and transcripts accumulate to high levels, irrespective of oxygen availability. We have examined the expression pattern of pyruvate decarboxylase and alcohol dehydrogenase at the protein level in developing pollen and show that the active proteins are localized to the gametophytic tissue and begin to accumulate at microspore mitosis. A flux through the ethanolic fermentation pathway could already be detected very early in pollen development, occurring in all stages from premeiotic buds to mature pollen. This flux was primarily controlled not by oxygen availability, but rather by sugar supply. At a high rate of sugar metabolism, respiration and fermentation took place concurrently in developing and germinating pollen. We propose that aerobic fermentation provides a shunt from pyruvate to acetyl-CoA to accommodate the increased demand for energy and biosynthetic intermediates during pollen development and germination. A possible undesirable side-effect is the potential accumulation of toxic acetaldehyde. Our results support a model for cms-T-type male sterility in maize, in which degeneration of the tapetum is caused by the toxic effects of acetaldehyde on mitochondria weakened by the presence of the URF13 protein.

Aerobiosis↗

PubMed1998

Application of alpha-keto acid decarboxylases in biotransformations.

The advantages of using enzymes in the synthesis of organic compounds relate to their versatility, high reaction rates, and regio- and stereospecificity and the relatively mild reaction conditions involved. Stereospecificity is especially important in the synthesis of bioactive molecules, as only one of the enantiomeric forms usually manifests bioactivity, whereas the other is often toxic. Although enzymes which catalyze asymmetric carbon-carbon bond formation are of great importance in bioorganic chemistry, only a few examples are known for thiamin diphosphate (ThDP)-dependent enzymes, whereas transformations using e.g. aldolases, lipases and lyases are well documented already. The present review surveys recent work on the application of pyruvate decarboxylase and benzoylformate decarboxylase in organic synthesis. These enzymes catalyze the synthesis of chiral alpha-hydroxy ketones which are versatile building blocks for organic and pharmaceutical chemistry. Besides the substrate spectra of both enzymes amino acid residues relevant for substrate specificity and enantioselectivity of pyruvate decarboxylase have been investigated by site-directed mutagenesis.

Amino Acid Sequence↗

PubMed1996

ERA, a novel cis-acting element required for autoregulation and ethanol repression of PDC1 transcription in Saccharomyces cerevisiae.

Yeast pyruvate decarboxylase (Pdc) catalyses the reaction at the branch-point of fermentation and respiration. In this work we have investigated the mechanisms of its transcriptional regulation in response to glucose and the non-fermentable carbon source ethanol. For this purpose we studied the function of different promoter fragments of PDC1, encoding the major pyruvate decarboxylase enzyme in wild-type cells, in the basal CYC1 promoter context. Thus, we identified a sequence mediating the response to ethanol and provide evidence showing that transcription of PDC1 is controlled by ethanol repression rather than by glucose induction. Furthermore, we showed that the same sequence is responsible for an autoregulatory process, leading to increased transcription from both the PDC1 and the PDC5 promoters, in strains in which the genomic copy of PDC1 is deleted. In addition, we have confirmed the role of Rap1 binding and have demonstrated that the Gcr1 protein also acts in transcriptional activation. DNA-protein interactions at the consensus Rap1-binding site and the newly identified ethanol-repression sequence (5'-AAATGCATA-3', termed 'ERA') were investigated by gel-shift and footprint analyses. Both DNA-binding activities were found in extracts from cells grown in media containing glucose or ethanol as the carbon source, indicating that the capacity to bind is not altered by the carbon source used.

DNA Footprinting↗

PubMed1998

Effect of specific growth rate on fermentative capacity of baker's yeast.

The specific growth rate is a key control parameter in the industrial production of baker's yeast. Nevertheless, quantitative data describing its effect on fermentative capacity are not available from the literature. In this study, the effect of the specific growth rate on the physiology and fermentative capacity of an industrial Saccharomyces cerevisiae strain in aerobic, glucose-limited chemostat cultures was investigated. At specific growth rates (dilution rates, D) below 0.28 h-1, glucose metabolism was fully respiratory. Above this dilution rate, respirofermentative metabolism set in, with ethanol production rates of up to 14 mmol of ethanol . g of biomass-1 . h-1 at D = 0.40 h-1. A substantial fermentative capacity (assayed offline as ethanol production rate under anaerobic conditions) was found in cultures in which no ethanol was detectable (D < 0.28 h-1). This fermentative capacity increased with increasing dilution rates, from 10.0 mmol of ethanol . g of dry yeast biomass-1 . h-1 at D = 0.025 h-1 to 20.5 mmol of ethanol . g of dry yeast biomass-1 . h-1 at D = 0.28 h-1. At even higher dilution rates, the fermentative capacity showed only a small further increase, up to 22.0 mmol of ethanol . g of dry yeast biomass-1 . h-1 at D = 0.40 h-1. The activities of all glycolytic enzymes, pyruvate decarboxylase, and alcohol dehydrogenase were determined in cell extracts. Only the in vitro activities of pyruvate decarboxylase and phosphofructokinase showed a clear positive correlation with fermentative capacity. These enzymes are interesting targets for overexpression in attempts to improve the fermentative capacity of aerobic cultures grown at low specific growth rates.

Acetates↗

PubMed1992

Enzyme activities of D-glucose metabolism in the fission yeast Schizosaccharomyces pombe.

The activities of key enzymes that are members of D-glucose metabolic pathways in Schizosaccharomyces pombe undergoing respirative, respirofermentative, and fermentative metabolisms are monitored. The steady-state activities of glycolytic enzymes, except phosphofructokinase, decrease with a reduced efficiency in D-glucose utilization by yeast continuous culture. On the other hand, the enzymic activities of pentose monophosphate pathway reach the maximum when the cell mass production of the cultures is optimum. Enzymes of tricarboxylate cycle exhibit the maximum activities at approximately the washout rate. The steady-state activity of pyruvate dehydrogenase complex increases rapidly when D-glucose is efficiently utilized. By comparison, the activity of pyruvate decarboxylase begins to increase only when ethanol production occurs. Depletion of dissolved oxygen suppresses the activity of pyruvate dehydrogenase complex but facilitates that of pyruvate decarboxylase. Acetate greatly enhances the acetyl CoA synthetase activity. Similarly, ethanol stimulates alcohol dehydrogenase and aldehyde dehydrogenase activities. Evidence for the existence of alcohol dehydrogenase isozymes in the fission yeast is presented.

Cell Division↗

PubMed1988

Sensitivity of yeast glycolytic enzymes to chloroquine.

Chloroquine at pH 8.0 and 1mM [corrected] concentration inhibits about 30% glucose consumption and ethanol formation in yeast cells. Out of the 11 glycolytic enzymes assayed, phosphoglycerate kinase and pyruvate decarboxylase have been found to be most sensitive to chloroquine. Next sensitive are hexokinase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase. Kinetic studies with the three kinases studied revealed competitive inhibition of chloroquine with ATP (hexokinase, phosphoglycerate kinase) or ADP (pyruvate kinase).

Adenosine Diphosphate↗

PubMed1997

Changes in the growth and enzyme level of Zymomonas mobilis under oxygen-limited conditions at low glucose concentration.

Zymomonas mobilis growing aerobically with 20 g glucose-1 (carbon-limited) in a chemostat exhibited an increase in both the molar growth yield (Yx/s) and the maximum molar growth yield (Yx/smax) and a decrease in both the specific substrate consumption rate (qs) and the maintenance energy consumption rate (me). Stepwise increase in the input oxygen partial pressure showed that anaerobic-to-aerobic transitional adaptation occurred in four stages: anaerobic (0 mm HgO2), oxygen-limited (7.6- 230 mm HgO2), intermediate (273 mm HgO2), and oxygen excess (290 mm HgO2). The steady-state biomass concentration, Yx/s, and intracellular ATP content increased between oxygen partial pressures of 7.6 and 120 mm HgO2, accompanied by a decrease in the qs and the specific acid production rate. The membrane ATPase activity decreased with increasing oxygen partial pressure and reached its lowest levels at 273 mm HgO2, which was the highest input oxygen partial pressure where steady-state conditions were possible. Glucokinase, glucose-6-phosphate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, and alcohol dehydrogenase activities also decreased when the oxygen partial pressure was increased above 15 mm Hg, whereas pyruvate decarboxylase was unaffected by aeration. Growth inhibition at 290 mm HgO2 was characterised by a drastic reduction in the pyruvate kinase activity and a collapse in the intracellular ATP pool. The growth and enzyme data suggest that at low glucose concentrations and oxygen-limited conditions, the increase in biomass yields is a reflection of a redirection of ATP usage rather than a net increase in energy production.

Adenosine Triphosphatases↗

PubMed1994

Demonstration of the indolepyruvate decarboxylase gene homologue in different auxin-producing species of the Enterobacteriaceae.

Different Enterobacteriaceae were assayed for their ability to produce the plant hormone indole-3-acetate with the aim to study the distribution of the indole-3-pyruvate pathway, which is known to be involved in the production of indole-3-acetate in a root-associated Enterobacter cloacae strain. Other E. cloacae strains, and also Enterobacter agglomerans strains, Pantoea agglomerans, Klebsiella aerogenes, and Klebsiella oxytoca were found to convert tryptophan into indole-3-acetate. As it was also intended to identify the conserved regions of the indole-3-pyruvate decarboxylase, which is involved in producing indole-3-acetate in the E. cloacae strain, oligonucleotide primers were synthesized for different regions of the corresponding gene. One pair of these primers allowed us to amplify a segment of the predicted size by the polymerase chain reaction with DNA of the seven different Enterobacteriaceae that produce indole-3-acetate. Segments of five strains were cloned and sequenced. All sequences showed significant homology to the indole-3-pyruvate decarboxylase gene. As in addition a positive DNA-DNA hybridization signal was detected in the seven strains using the E. cloacae or E. agglomerans segments as a probe, indole-3-acetate biosynthesis is suggested to be catalyzed via the indole-3-pyruvate pathway not only in E. cloacae but also in the other soil-living Enterobacteriaceae. Conserved regions were detected in the indole-3-decarboxylase by alignment of the now-available five different partial sequences. These regions should enable identification of the gene in other bacterial families or even in plants.

Amino Acid Sequence↗

PubMed2003

Localization of sucrose synthase in wheat roots: increased in situ activity of sucrose synthase correlates with cell wall thickening by cellulose deposition under hypoxia.

Sucrose synthase (SuSy; EC 2.4.1.13) plays a prominent role in O(2) deficiency and functions at a branch point, partitioning sucrose between cell wall biosynthesis and glycolysis. The cleavage of sucrose by SuSy was localized in wheat ( Triticum aestivum L. cv. Alcedo) roots subjected to 4 days of hypoxia. Increased SuSy activity was observed by in situ activity staining in the tip region and in the stele of root axes. The pattern of cellulose deposition correlated with regions of high SuSy activity. Cellulose accounted for more than 30% of root dry weight and the cellulose content increased substantially under hypoxia. The strongest accumulation of cellulose occurred in the base and mid-regions of the roots where the content rose to 163% and 182% of controls, respectively. In the root axis, cellulose deposition occurred in the endodermis and walls of pith cells. In root tips, cellulose was primarily deposited in developing xylem and phloem. The marker enzyme for O(2) shortage, pyruvate decarboxylase (EC 4.1.1.17), exhibited a 14-fold increase in the root apex, whereas in basal root tissues, which contained more aerenchyma, pyruvate decarboxylase activity was only doubled. The root apex also contained the highest concentration of sucrose and hexoses. The elevated sugar content in all root zones was partially used to synthesize cellulose for secondary wall thickening.

Cell Wall↗

PubMed1999

Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases.

When the E91D variant of apo-yeast pyruvate decarboxylase (EC 4.1.1. 1) is exposed to C2alpha-hydroxybenzylthiamin diphosphate, this putative intermediate is partitioned on the enzyme between release of the benzaldehyde product (as evidenced by regeneration of active enzyme) and dissociation of the proton at C2alpha to form the enamine-C2alpha-carbanion intermediate. While the pKa (the negative log of the acid dissociation constant) for this dissociation is approximately 15.4 in water, formation of the enamine at pH 6.0 on the enzyme indicates a >9 unit pKa suppression by the enzyme environment. The dramatic stabilization of this zwitterionic enamine intermediate at the active center is sufficient to account for as much as a 10(9)-fold rate acceleration on the enzyme. This "solvent" effect could be useful for achieving the bulk of the rate acceleration provided by the protein over and above that afforded by the coenzyme on all thiamin diphosphate-dependent 2-oxo acid decarboxylases.

Binding Sites↗

PubMed1991

Expression of an L-alanine dehydrogenase gene in Zymomonas mobilis and excretion of L-alanine.

An approach to broaden the product range of the ethanologenic, gram-negative bacterium Zymomonas mobilis by means of genetic engineering is presented. Gene alaD for L-alanine dehydrogenase (EC 1.4.1.1.) from Bacillus sphaericus was cloned and introduced into Z. mobilis. Under the control of the strong promoter of the pyruvate decarboxylase (pdc) gene, the enzyme was expressed up to a specific activity of nearly 1 mu mol . min -1 . mg of protein -1 in recombinant cells. As a results of this high L-alanine dehydrogenase activity, growing cells excreted up to 10 mmol of alanine per 280 mmol of glucose utilized into a mineral salts medium. By the addition of 85 mM NH4+ to the medium, growth of the recombinant cells stopped, and up to 41 mmol alanine was secreted. As alanine dehydrogenase competed with pyruvate decarboxylase (PDC) (EC 4.1.1.1.) for the same substrate (pyruvate), PDC activity was reduced by starvation for the essential PDC cofactor thiamine PPi. A thiamine auxotrophy mutant of Z. mobilis which carried the alaD gene was starved for 40 h in glucose-supplemented mineral salts medium and then shifted to mineral salts medium with 85 mM NH4+ and 280 mmol of glucose. The recombinants excreted up to 84 mmol of alanine (7.5 g/liter) over 25 h. Alanine excretion proceeded at an initial velocity of 238 nmol . min-1 . mg [dry weight]-1. Despite this high activity, the excretion rate seemed to be a limiting factor, as the intracellular concentration of alanine was as high as 260 mM at the beginning of the excretion phase and decreased to 80 to 90 mM over 24 h.

Alanine↗

PubMed2003

Interactions of the peripheral subunit-binding domain of the dihydrolipoyl acetyltransferase component in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.

The enzymes pyruvate decarboxylase (E1) and dihydrolipoyl dehydrogenase (E3) bind tightly but in a mutually exclusive manner to the peripheral subunit-binding domain (PSBD) of dihydrolipoyl acetyltransferase in the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. The use of directed mutagenesis, surface plasmon resonance detection and isothermal titration microcalorimetry revealed that several positively charged residues of the PSBD, most notably Arg135, play an important part in the interaction with both E1 and E3, whereas Met131 makes a significant contribution to the binding of E1 only. This indicates that the binding sites for E1 and E3 on the PSBD are overlapping but probably significantly different, and that additional hydrophobic interactions may be involved in binding E1 compared with E3. Arg135 of the PSBD was also replaced with cysteine (R135C), which was then modified chemically by alkylation with increasingly large aliphatic groups (R135C -methyl, -ethyl, -propyl and -butyl). The pattern of changes in the values of DeltaG degrees, DeltaH degrees and TDeltaS degrees that were found to accompany the interaction with the variant PSBDs differed between E1 and E3 despite the similarities in the free energies of their binding to the wild-type. The importance of a positive charge on the side-chain at position 135 for the interaction of the PSBD with E3 and E1 was apparent, although lysine was found to be an imperfect substitute for arginine. The results offer further evidence of entropy-enthalpy compensation ('thermodynamic homeostasis') - a feature of systems involving a multiplicity of weak interactions.

Acetyltransferases↗

PubMed1988

Acetolactate Synthase Activity in Developing Maize (Zea mays L.) Kernels.

Acetolactate synthase (EC 4.1.3.18) activity was examined in maize (Zea mays L.) endosperm and embryos as a function of kernel development. When assayed using unpurified homogenates, embryo acetolactate synthase activity appeared less sensitive to inhibition by leucine + valine and by the imidazolinone herbicide imazapyr than endosperm acetolactate synthase activity. Evidence is presented to show that pyruvate decarboxylase contributes to apparent acetolactate synthase activity in crude embryo extracts and a modification of the acetolactate synthase assay is proposed to correct for the presence of pyruvate decarboxylase in unpurified plant homogenates. Endosperm acetolactate synthase activity increased rapidly during early kernel development, reaching a maximum of 3 micromoles acetoin per hour per endosperm at 25 days after pollination. In contrast, embryo activity was low in young kernels and steadily increased throughout development to a maximum activity of 0.24 micromole per hour per embryo by 45 days after pollination. The sensitivity of both endosperm and embryo acetolactate synthase activities to feedback inhibition by leucine + valine did not change during kernel development. The results are compared to those found for other enzymes of nitrogen metabolism and discussed with respect to the potential roles of the embryo and endosperm in providing amino acids for storage protein synthesis.

Journal Article↗

PubMed1995

Glucose metabolism, enzymic analysis and product formation in chemostat culture of Hanseniaspora uvarum.

The physiology of Hanseniaspora uvarum K5 was studied in glucose-limited chemostat cultures and upon glucose pulse. Up to a dilution rate of 0.28 h-1, glucose was completely metabolized in biomass and CO2. Above this value, increase in the dilution rate was accompanied by sequential production of metabolites (glycerol, acetate and ethanol) and decrease in cell yield. Similar results were observed upon glucose pulse. From the enzyme activities (pyruvate dehydrogenase, pyruvate decarboxylase, NAD and NADP-dependent acetaldehyde dehydrogenases, acetyl coenzyme A synthetase and alcohol dehydrogenase) and substrate affinities, the following conclusions were drawn with respect to product formation of cells: (1) pyruvate was preferentially metabolized via pyruvate dehydrogenase, when biomass and CO2 were the only products formed; (2) acetaldehyde formed by pyruvate decarboxylase was preferentially oxidized in acetate by NADP-dependent aldehyde dehydrogenase; acetate accumulation results from insufficient activity of acetyl-CoA synthetase required for the complete oxidation of acetate; (3) acetaldehyde was oxidized in ethanol by alcohol dehydrogenase, in addition to acetate production.

Acetates↗