Molecular-genetic and biochemical characteristics of citrate synthase from the citric-acid producing fungus <Emphasis Type="Italic">Aspergillus niger</Emphasis>

This review is devoted to achievements in the study of citrate synthase, an enzyme that plays a key role in cell metabolism and catalyzes the process of citric acid synthesis at the first step of the tricarboxylic acid cycle (TCA). The primary industrial producer of citric acid is Aspergillus niger fungus; therefore, the fundamental molecular-genetic and biochemical characteristics of the enzyme from this producer are discussed in comparison with those of other eukaryotes. The information on the mechanisms of the citric acid overproduction in A. niger and its evolutionary features is analyzed. The current review can be helpful in the development of a strategy for the design of more effective producers of organic acids.     

3-Isopropylmalate is the major endogenous substrate of the Saccharomyces cerevisiae trans-aconitate methyltransferase

The Saccharomyces cerevisiae Tmt1 gene product is the yeast homologue of the Escherichia coli enzyme that catalyzes the methyl esterification of trans-aconitate, a thermodynamically favored isomer of cis-aconitate and an inhibitor of the citric acid cycle. It has been proposed that methylation may attenuate trans-aconitate inhibition of aconitase and other enzymes of the cycle. Although trans-aconitate is a minor endogenous substrate of the Tmt1 enzyme in extracts of S. cerevisiae, the major endogenous substrate has yet to be identified. We show here that a trimethylsilylated derivative of the major methylated endogenous product of Tmt1 in yeast extracts has an identical gas chromatography retention time and an identical electron impact mass spectrum as one of the two possible monomethyl ester derivatives of (2R,3S)-3-isopropylmalate. (2R,3S)-3-Isopropylmalate is an intermediate of the leucine biosynthetic pathway that shares similar intermediates and reaction chemistry with the portion of the citric acid cycle from oxaloacetate to alpha-ketoglutarate via cis-aconitate. The Tmt1 methyltransferase recognizes (2R,3S)-3-isopropylmalate with similar kinetics as it does trans-aconitate, with respective K(m) values of 127 and 53 microM and V(max) values of 59 and 70 nmol min(-1) mg(-1) of protein in a Tmt1-overexpressed yeast extract. However, we found that isopropylfumarate, the direct homologue of trans-aconitate in the leucine biosynthetic pathway, was at best a very poor substrate for the Tmt1 yeast enzyme. Similarly, the direct homologue of 3-isopropylmalate in the citric acid cycle, isocitrate, is also a very poor substrate. This apparent change in specificity between the intermediates of these two pathways can be understood in terms of the binding of these substrates to the active site. These results suggest that the Tmt1 methyltransferase may work in two different pathways in two different ways: for detoxification in the citric acid cycle and for a possibly novel biosynthetic branch reaction of the leucine biosynthetic pathway.     

The synthesis of glutamic acid in the absence of enzymes: Implications for biogenesis

This paper reports on the non-enzymatic aqueous phase synthesis of amino acids from keto acids, ammonia and reducing agents. The facile synthesis of key metabolic intermediates, particularly in the glycolytic pathway, the citric acid cycle, and the first step of amino acid synthesis, lead to new ways of looking at the problem of biogenesis.     

Differences between mouse and rat pancreatic islets: succinate responsiveness,malic enzyme,and anaplerosis

Succinic acid methyl esters are potent insulin secretagogues in rat pancreatic islets, but they do not stimulate insulin release in mouse islets. Unlike rat and human islets, mouse islets lack malic enzyme and, therefore, are unable to form pyruvate from succinate-derived malate for net synthesis of acetyl-CoA. Dimethyl-[2,3-(14)C]succinate is metabolized in the citric acid cycle in mouse islets to the same extent as in rat islets, indicating that endogenous acetyl-CoA condenses with oxaloacetate derived from succinate. However, without malic enzyme, the net synthesis from succinate of the citric acid cycle intermediates citrate, isocitrate, and alpha-ketoglutarate cannot occur. Glucose and other nutrients that augment alpha-ketoglutarate formation are secretagogues in mouse islets with potencies similar to those in rat islets. All cycle intermediates can be net-synthesized from alpha-ketoglutarate. Rotenone, an inhibitor of site I of the electron transport chain, inhibits methyl succinate-induced insulin release in rat islets even though succinate oxidation forms ATP at sites II and III of the respiratory chain. Thus generating ATP, NADH, and anaplerosis of succinyl-CoA plus the four-carbon dicarboxylic acids of the cycle and its metabolism in the citric acid cycle is insufficient for a fuel to be insulinotropic; it must additionally promote anaplerosis of alpha-ketoglutarate or two intermediates interconvertible with alpha-ketoglutarate, citrate, and isocitrate.     

A Highlights from MBoC Selection: The novel component Kgd4 recruits the E3 subunit to the mitochondrial α-ketoglutarate dehydrogenase

The mitochondrial citric acid cycle is a central hub of cellular metabolism, providing intermediates for biosynthetic pathways and channeling electrons to the respiratory chain complexes. In this study, we elucidated the composition and organization of the multienzyme complex α-ketoglutarate dehydrogenase (α-KGDH). In addition to the three classical E1-E3 subunits, we identified a novel component, Kgd4 (Ymr31/MRPS36), which was previously assigned to be a subunit of the mitochondrial ribosome. Biochemical analyses demonstrate that this protein plays an evolutionarily conserved role in the organization of mitochondrial α-KGDH complexes of fungi and animals. By binding to both the E1-E2 core and the E3 subunit, Kgd4 acts as a molecular adaptor that is necessary to a form a stable α-KGDH enzyme complex. Our work thus reveals a novel subunit of a key citric acid–cycle enzyme and shows how this large complex is organized.     

Changes in primary metabolism leading to citric acid overflow in <Emphasis Type="Italic">Aspergillus niger</Emphasis>

For citric acid-accumulating Aspergillus niger cells, the enhancement of anaplerotic reactions replenishing tricarboxylic acid cycle intermediates predisposes the cells to form the product. However, there is no increased citrate level in germinating spores and a complex sequence of developmental events is needed to change the metabolism in a way that leads to an increased level of tricarboxylic acid cycle intermediates in mycelia. A review of physiological events that cause such intracellular conditions, with the special emphasis on the discussion of hexose transport into the cells and regulation of primary metabolism, predominantly of glycolytic flux during the process, is presented.     

The energetics of the reductive citric acid cycle in the pyrite-pulled surface metabolism in the early stage of evolution

The chemoautotrophic theory concerning the origin of life postulates that a central role is played in the prebiotic chemical machinery by a reductive citric acid cycle operating without enzymes. The crucial point in this scenario is the formation of pyrite from hydrogen sulfide and ferrous sulfide, a reaction suggested to be linked to endergonic reactions, making them exergonic. This mechanism is believed to provide the driving force for the cycle to operate as a carbon dioxide fixation network. The present paper criticizes the thermodynamic calculations and their presentation in the original version of the archaic reductive citric acid cycle [W?chtersh?user, 1990. Evolution of the first metabolic cycles. Proc. Natl Acad. Sci. USA 87, 200-204.]. The most significant differences between the W?chtersh?user hypothesis and the present proposal: W?chtersh?user did not consider individual reactions in his calculations. A particularly questionable feature is the involvement of seven molecules of pyrite which does not emerge as a direct consequence of the chemical reactions presented in the archaic reductive citric acid cycle. The involvement of a considerable number of sulfur-containing organic intermediates as building blocks is also disputed. In the new scheme of the cycle proposed here, less free energy is liberated than hypothesized by W?chtersh?user, but it has the advantages that the free energy changes for the individual reactions can be calculated, the number of pyrite molecules involved in the cycle is reduced, and fewer sulfur-containing intermediates are required for the cycle to operate. In combination with a plausible route for the anaplerotic reactions [Kalapos, 1997a. Possible evolutionary role of methylglyoxalase pathway: anaplerotic route for reductive citric acid cycle of surface metabolists. J. Theor. Biol. 188, 201-206.], this new presentation of the cycle assigns a special meaning to hydrogen sulfide formation in the early stage of biochemical evolution.     

A heme-deficient strain of Escherichia coli has a three-base pair deletion in a "hotspot" in hemA

The key regulatory step in heme biosynthesis in Escherichia coli is at the level of glutamyl-tRNA reductase (GTR), an enzyme which is encoded by hemA. A strain, HU227, with a spontaneous in-frame mutation in hemA has no GTR activity. The mutation is shown to be a three-base deletion at a "hotspot" in the gene. The amino acid sequence in this region is highly conserved.     

CARBOHYDRATE AND AMINO ACID METABOLISM IN RAT CEREBRAL CORTEX IN MODERATE AND EXTREME HYPERCAPNIA

—The time course of changes in glycolytic and citric acid cycle intermediates and in amino acids was studied in acute and steady state hypercapnia. Experiments on unanaesthetized animals exposed to 10% CO₂ for 10, 20 and 60s showed that there was a transient decrease in glycogen concentration, progressive increases in glucose-6-phosphate and fructose-6-phosphate and decreases in pyruvate and lactate. During this time the levels of amino acids and Krebs cycle intermediates did not change, except for a small fall in malate at 60s. The results indicate that there was a decrease in glycolytic flux due to an inhibition of the phosphofructokinase reaction. Since the tissue levels of phosphocreatine, ATP, ADP and AMP were unchanged inhibition of phosphofructokinase was probably due to the fall in pH. Anaesthetized animals were exposed to about 5% CO₂ (for 2, 5, 15, 30 and 60 min) or to about 45% CO₂ (for 5 and 15 min). Except for succinate, which increased, all citric acid cycle metabolites analysed (citrate, α-ketoglutarate, fumarate and malate) decreased with the rise in CO₂-tension. The sum of the amino acids analysed (glutamate, glutamine, aspartate, asparagine, alanine and GABA) decreased at extreme hypercapnia. The results suggest that Krebs cycle intermediates and amino acids are partly used as substrates for energy production when there is reduced pyruvate availability due to hypercapnia. It is proposed that amino acid carbon is made available for oxidation via transamination (aspartate aminotransferase reaction) and deamination (glutamate dehydrogenase reaction) and that citric acid cycle intermediates are metabolized following a reversal of reactions usually leading to CO₂ fixation.     

Formation of the "peroxy" intermediate in cytochrome c oxidase is associated with internal proton/hydrogen transfer

When dioxygen is reduced to water by cytochrome c oxidase a sequence of oxygen intermediates are formed at the reaction site. One of these intermediates is called the "peroxy" (P) intermediate. It can be formed by reacting the two-electron reduced (mixed-valence) cytochrome c oxidase with dioxygen (called P(m)), but it is also formed transiently during the reaction of the fully reduced enzyme with oxygen (called P(r)). In recent years, evidence has accumulated to suggest that the O-O bond is cleaved in the P intermediate and that the heme a(3) iron is in the oxo-ferryl state. In this study, we have investigated the kinetic and thermodynamic parameters for formation of P(m) and P(r), respectively, in the Rhodobacter sphaeroides enzyme. The rate constants and activation energies for the formation of the P(r) and P(m) intermediates were 1.4 x 10(4) s(-1) ( approximately 20 kJ/mol) and 3 x 10(3) s(-1) ( approximately 24 kJ/mol), respectively. The formation rates of both P intermediates were independent of pH in the range 6.5-9, and there was no proton uptake from solution during P formation. Nevertheless, formation of both P(m) and P(r) were slowed by a factor of 1.4-1.9 in D(2)O, which suggests that transfer of an internal proton or hydrogen atom is involved in the rate-limiting step of P formation. We discuss the origin of the difference in the formation rates of the P(m) and P(r) intermediates, the formation mechanisms of P(m)/P(r), and the involvement of these intermediates in proton pumping.     

Action of catalase on peroxyacetic acid. Kinetic studies

The activity of catalase on peroxoacetic acid was studied by a kinetic point of view. The "inactivation-reactivation" sequence consists in two first order (intramolecular) one-electron redox reactions. In the catalytic cycle, the reaction producing Compound I is, as espected, a second order process rate determined by the enzyme-peroxide adduct formation step, whereas, surprisingly, the reaction restoring the enzyme resting state is a first order process in which the limiting step is the 0-0 linkage breaking inside the Compound I-peroxide adduct.     

Regulation of NAD<Superscript>+</Superscript>-dependent isocitrate dehydrogenase in the citrate producing yeast <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis>

The mechanism of the increased accumulation (overproduction) of citric acids in the yeast Yarrowia lipolytica while growing in the presence of glucose under nitrogen deficiency was investigated. The limitation of the yeast growth by the source of nitrogen decreases the total content of nucleotides and increases the ratios of ATP/AMP and NADH/NAD⁺. NAD⁺-Dependent isocitrate dehydrogenase, an enzyme of the tricarboxylic acid cycle playing a key role in the regulation of biosynthesis of citric and isocitric acids, was isolated from Y. lipolytica. The molecular weights of the native enzyme and its subunits were found to be 412 and 52 kD, respectively. It is concluded that the enzyme is a homooligomer consisting of eight subunits. Investigation of the effect of some intermediates of the tricarboxylic acid cycle on the activity of this enzyme suggests that the enhanced excretion of citric acids can be caused by the inhibition of NAD⁺-dependent isocitrate dehydrogenase due to the decrease in the content of AMP and increase in the NADH/NAD⁺ ratio in the cells of Y. lipolytica under depletion of nitrogen.Translated from Biokhimiya, Vol. 69, No. 12, 2004, pp. 1706–1714.Original Russian Text Copyright © 2004 by Morgunov, Solodovnikova, Sharyshev, Kamzolova, Finogenova.     

Perspective: emerging evidence for signaling roles of mitochondrial anaplerotic products in insulin secretion

The importance of mitochondrial biosynthesis in stimulus secretion coupling in the insulin-producing beta-cell probably equals that of ATP production. In glucose-induced insulin secretion, the rate of pyruvate carboxylation is very high and correlates more strongly with the glucose concentration the beta-cell is exposed to (and thus with insulin release) than does pyruvate decarboxylation, which produces acetyl-CoA for metabolism in the citric acid cycle to produce ATP. The carboxylation pathway can increase the levels of citric acid cycle intermediates, and this indicates that anaplerosis, the net synthesis of cycle intermediates, is important for insulin secretion. Increased cycle intermediates will alter mitochondrial processes, and, therefore, the synthesized intermediates must be exported from mitochondria to the cytosol (cataplerosis). This further suggests that these intermediates have roles in signaling insulin secretion. Although evidence is quite good that all physiological fuel secretagogues stimulate insulin secretion via anaplerosis, evidence is just emerging about the possible extramitochondrial roles of exported citric acid cycle intermediates. This article speculates on their potential roles as signaling molecules themselves and as exporters of equivalents of NADPH, acetyl-CoA and malonyl-CoA, as well as alpha-ketoglutarate as a substrate for hydroxylases. We also discuss the "succinate mechanism," which hypothesizes that insulin secretagogues produce both NADPH and mevalonate. Finally, we discuss the role of mitochondria in causing oscillations in beta-cell citrate levels. These parallel oscillations in ATP and NAD(P)H. Oscillations in beta-cell plasma membrane electrical potential, ATP/ADP and NAD(P)/NAD(P)H ratios, and glycolytic flux are known to correlate with pulsatile insulin release. Citrate oscillations might synchronize oscillations of individual mitochondria with one another and mitochondrial oscillations with oscillations in glycolysis and, therefore, with flux of pyruvate into mitochondria. Thus citrate oscillations may synchronize mitochondrial ATP production and anaplerosis with other cellular oscillations.     

Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius

We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, d-xylose and l-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of d-xylose and l-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.     

On the action of carboxy groups in the citrate synthase reaction

The aza analogue (RS)-3-hydroxy-2,5-pyrrolidinedione-3-acetic acid (6) of the five-membered citric anhydride (2) was prepared in the sequence citric acid----2-phenyl-1,3-dioxolan-4-one-5,5-diacetic acid (1)----citric acid beta-amide (3)----6 and used to resolve ambiguities in the mechanism of the citrate synthase reaction. The results yield no indication for the formation of anhydride 2 on the enzyme and favour the direct hydrolysis of the intermediate (3S)-citryl-CoA. Ammonolysis of the dioxolanone 1 in the reaction sequence described above produced not only citric acid beta-amide but also the alpha-isomer. This is shown to originate in the transient formation of anhydride 2. Hydrolysis of the dioxolanone 1 under "physiological conditions" occurs via anhydride 2, generated in intramolecular bifunctional catalysis by a protonated and a deprotonated carboxyl group. The catalytic residue Asp375 of citrate synthase is considered to operate on the enzyme as does the protonated carboxyl group in the chemical reaction and to generate enolic acetyl-CoA in cooperative catalysis with His274. This reaction of Asp375 may also facilitate the hydrolysis of citryl-CoA.     

Biodegradation of bis(1-chloro-2-propyl) ether via initial ether scission and subsequent dehalogenation by<Emphasis Type="Italic"> Rhodococcus</Emphasis> sp. strain DTB

Rhodococcus sp. strain DTB (DSM 44534) grows on bis(1-chloro-2-propyl) ether (DDE) as sole source of carbon and energy. The non-chlorinated diisopropyl ether and bis(1-hydroxy-2-propyl) ether, however, did not serve as substrates. In ether degradation experiments with dense cell suspensions, 1-chloro-2-propanol and chloroacetone were formed, which indicated that scission of the ether bond is the first step while dehalogenation of the chlorinated C(3)-compounds occurs at a later stage of the degradation pathway. Inhibition of ether scission by methimazole suggested that the first step in degradation is catalyzed by a flavin-dependent enzyme activity. The non-chlorinated compounds 1,2-propanediol, hydroxyacetone, lactate, pyruvate, 1-propanol, propanal, and propionate also supported growth, which suggested that the intermediates 1,2-propanediol and hydroxyacetone are converted to pyruvate or to propionate, which can be channeled into the citric acid cycle by a number of routes. Total release of chloride and growth-yield experiments with DDE and non-chlorinated C(3)-compounds suggested complete biodegradation of the chlorinated ether.     

A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution

There are two fundamental axioms of surface metabolism theory: (i) pyrite formation from H2S and FeS is proposed as a source of energy for life, and (ii) archaic reductive citric acid cycle is put into the center of a metabolic network. However, the concept fails to indicate how sulfide oxidation ought to be coupled to processes driven by free energy change occurring during pyrite production, and secondly, how reductive citric acid cycle ought to be supplied with row material(s). Recently, the non-enzymatic methylglyoxalase pathway has been recommended as the anaplerotic route for the reductive citric acid cycle. In this paper a mechanism is proposed by which the oxidation of lactate, the essential step of the anaplerotic path, becomes possible and a coupling system between sulfide oxidation and endergonic reaction(s) is also presented. Oxidoreduction for other redox pairs is discussed too. It is concluded that the S(o)/H2S system may have been the clue to energy production at the early stage of evolution, as hydrogen sulfide produced by the metabolic network may have functioned as a coupling molecule between endergonic and exergonic reactions.     

An alternative to the glyoxylate shunt

A cycle remains a cycle only as long as the spokes of the wheel are not stolen. To keep the citric acid cycle going requires anaplerotic reactions such as the glyoxylate shunt to restore the cycle intermediates that are withdrawn for the biosynthesis of cell constituents, e.g. amino acids and haemin precursors. The article by Erb et al . in this issue of Molecular Microbiology documents an alternative path that replenishes four-carbon intermediates during growth on acetate in the absence of the glyoxylate shunt. The reaction sequence forms malate and succinyl-CoA from three acetyl-CoA, one CO₂ and one HCO₃ in a linear pathway. This new pathway was discovered in phototrophic anoxygenic bacteria and in few aerobic bacteria, but it is probably widespread among many metabolic groups of bacteria.     

Mechanism of acetate oxidation to CO2 with elemental sulfur in Desulfuromonas acetoxidans

The strict anaerobe Desulfuromonas acetoxidans can oxidize acetate to CO₂ with elemental sulfur as electron acceptor. ¹⁴C-labelling experiments and enzyme studies are described revealing that acetate oxidation proceeds via the citric acid cycle with the synthesis of oxaloacetate from acetate and 2 CO₂ via pyruvate as anaplerotic reaction. An oxidation of acetate via one carbon unit intermediates as proposed for anaerobic bacteria fermenting acetate to 2 CO₂ and 4 H₂ was excluded.Dedicated to Professor Dr. Gerhart Drews on the occasion of his 60th birthday     

Repression of sporulation in Bacillus subtilis by L-malate.

L-Malate repressed sporulation in the wild-type strain of Bacillus subtilis. When 75 mM L-malate was added to the growth medium at the time of inoculation, the appearance of heat-resistant spores was delayed 6 to 8 h. The synthesis of extracellular serine protease, alkaline phosphatase, glucose dehydrogenase, and dipicolinic acid was similarly delayed. Sporulation was not repressed when malate was added to the culture at t4 or later. A mutant was selected for ability to sporulate in the presence of malate. This strain could also sporulate in the presence of glucose. The malate-resistant mutant grew poorly with malate as sole carbon source, although it possessed an intact citric acid cycle, and it showed increased levels of malic enzyme. This indicates a defect in the metabolism of malate in the mutant. A mutant lacking malate dehydrogenase activity was also able to sporulate in the presence of malate. A model for the regulation of sporulation by malate is presented and discussed. Citric acid cycle intermediates other than malate did not affect sporulation. In contrast to previous results, sporulation of certain citric acid cycle mutants could be greatly increased or completely restored by the addition of intermediates after the enzymatic block. The results indicate that the failure of citric acid cycle mutants to sporulate can be adequately explained by lack of energy and lack of glutamate.