Naturally occurring 1,3,4,6-hexanetetracarboxylic acid has meso stereochemistry

1,3,4,6-Hexanetetracarboxylic acid was first identified as a natural product during the structural characterization of methanofuran, one of several coenzymes involved in methanogenesis. A combination of high resolution ¹H NMR, ¹³C NMR, and gas chromatography-mass spectrometry has been used to establish that the naturally occurring diastereomer of 1,3,4,6-hexanetetracarboxylic acid in methanogenic Archaea is meso. © 1996 Wiley-Liss, Inc.     

Methanofuran (carbon dioxide reduction factor), a formyl carrier in methane production from carbon dioxide in Methanobacterium

Methanofuran (carbon dioxide reduction factor) became labeled when incubated in cell extracts of Methanobacterium under hydrogen and 14CO2 in the absence of methanopterin. Proton NMR spectroscopy revealed that a formyl group was bound to the primary amine of methanofuran. [14C]Formylmethanofuran was enzymically converted to 14CH4 in the presence of CH3-S-CoM [2-(methylthio)ethanesulfonic acid], hydrogen, and methanopterin, establishing the formyl moiety as an intermediate in methanogenesis. In the absence of methanopterin, a substantial portion of the formyl label was oxidized to 14CO2 rather than reduced to 14CH4, consistent with a model in which the C1 intermediate is first bound to methanofuran and then to methanopterin, during its reduction. When CH3-S-CoM was replaced by HS-CoM (2-mercaptoethanesulfonic acid), most of the formyl label was oxidized to 14CO2, indicating that methyl group reduction by the CH3-S-CoM methylreductase is required for the conversion of formylmethanofuran to methane.     

Identification, Biosynthesis, and Function of 1,3,4,6-Hexanetetracarboxylic Acid in Methanobacterium thermoautotrophicum DeltaH

An unusual compound, 1,3,4,6-hexanetetracarboxylic acid, was identified by H and C two-dimensional nuclear magnetic resonance spectroscopy and gas chromatography-mass spectrometry as one of the major components of the small-molecule pool in Methanobacterium thermoautotrophicum DeltaH under optimal conditions of cell growth. Incorporation of C- and H-labeled acetates was consistent with the biosynthesis of this tetracarboxylic acid from alpha-ketoglutarate, two molecules of acetyl-coenzyme A, and one molecule of CO(2), as established for the tetracarboxylic acid moiety of methanofuran. CO(2) pulse- CO(2) chase methodology was used to establish the turnover rate for this compound. In contrast to the two other major solutes in this bacterium, cyclic 2,3-diphosphoglycerate and glutamate, which are key metabolic intermediates, this free tetracarboxylic acid was metabolically inactive, with a half-life that exceeded the cell doubling time. Hence, this molecular pool cannot serve as a metabolic intermediate in cell biosynthesis. The functional role of free tetracarboxylate as a conservative part of a system that maintains high positive internal osmotic pressure in this bacterium is proposed.     

Structural characteristics of methanogenic cofactors in the non-methanogenic archaebacterium Archaeoglobus fulgidus

Archaeoglobus fulgidus is an extremely thermophilic, sulphate reducing archaebacterium thought to represent a biochemical missing-link between sulphur-metabolizing bacteria and methanogenic bacteria. Whereas the phylogenetic position of A.fulgidus is closer to the sulphur-metabolizing bacteria, there is a partial overlap in the biochemical machinery of A.fulgidus with both groups of bacteria. In particular, the presence of a number of aberrant cofactors up to now thought to be involved exclusively in the process of methanogenesis in methanogenic archaebacteria, i.e. coenzyme F420, methanofuran and methanopterin, has been indicated by previous studies. Here we present evidence for the structural identity of the methanopterin cofactor of A.fulgidus with the methanopterin isolated from Methanobacterium thermoautotrophicum and show that this non-methanogenic bacterium contains two as yet unknown analogues of coenzyme F420. The levels of the various cofactors were determined in cultures grown either on formate or lactate as the carbon source and sulphate or thiosulphate as the sulphur source.     

Regulation by nicotinic acid of malate dehydrogenase activity in tissues of Black Sea mussels

Nicotinic acid was studied for its effect on the malate dehydrogenase activity from mussels' tissues and on its ability to link substrate and coenzyme. NADH and nicotinic acid in high concentrations are shown to produce an inhibiting effect on the reverse malate dehydrogenase reaction which is determined by the nonspecific action either of the vitamin or its metabolites. When pH of the medium is shifted toward the acid zone the affinity of the enzyme to the coenzyme decreases. This phenomenon may be one of the mechanisms of the mussel organism adaptation to anaerobiosis.     

Highly active mutants of carbonyl reductase S1 with inverted coenzyme specificity and production of optically active alcohols

A wild type NADPH-dependent carbonyl reductase from Candida magnoliae (reductase S1) has been found not to utilize NADH as a coenzyme. A mutation to exchange the coenzyme specificity in reductase S1 has been designed by computer-aided methods, including three-dimensional structure modeling and in silico screening of enzyme mutants. Site-directed mutagenesis has been used to introduce systematic substitutions of seven or eight amino acid residues onto the adenosine-binding pocket of the enzyme according to rational computational design. The resulting S1 mutants show NADH-dependency and have lost their ability to utilize NADPH as a coenzyme, but retain those catalytic activities. Kinetic parameter V(max) and K(m) values of those mutants for NADH are 1/3- to 1/10-fold those of the wild type enzyme for NADPH. As a model system for industrial production of optically active alcohols, the S1 mutants can be applied to an asymmetric reduction of ketones, cooperating with a coenzyme-regeneration system that uses an NAD-dependent formate dehydrogenase.     

Identification of the gene encoding sulfopyruvate decarboxylase, an enzyme involved in biosynthesis of coenzyme M

The products of two adjacent genes in the chromosome of Methanococcus jannaschii are similar to the amino and carboxyl halves of phosphonopyruvate decarboxylase, the enzyme that catalyzes the second step of fosfomycin biosynthesis in Streptomyces wedmorensis. These two M. jannaschii genes were recombinantly expressed in Escherichia coli, and their gene products were tested for the ability to catalyze the decarboxylation of a series of alpha-ketoacids. Both subunits are required to form an alpha(6)beta(6) dodecamer that specifically catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde. This transformation is the fourth step in the biosynthesis of coenzyme M, a crucial cofactor in methanogenesis and aliphatic alkene metabolism. The M. jannaschii sulfopyruvate decarboxylase was found to be inactivated by oxygen and reactivated by reduction with dithionite. The two subunits, designated ComD and ComE, comprise the first enzyme for the biosynthesis of coenzyme M to be described.     

Derivatives of methanopterin, a coenzyme involved in methanogenesis

Degradational studies of methanopterin, a coenzyme involved in methanogenesis, are reported. The results of these studies are in full accordance with the proposed structure of methanopterin as N-[1'-(2'-amino-4'-hydroxy-7' -methyl-6'-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'-1' )O-alpha-ribofuranosyl-5'-phosphoric acid] aniline in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Acid hydrolysis of methanopterin cleaved the 5'----1' glycosidic bond and yielded a 'hydrolytic product' which was identified as N-[1'-(2'-amino-4'-hydroxy-7' -methyl-6'-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl]aniline. Alkaline permanganate oxidation of methanopterin yielded 7-methylpterin-6-carboxylic acid. Catalytic (or enzymatic) hydrogenation of methanopterin gave a mixture of 6-ethyl-7-methyl-7,8-dihydropterin, 6-ethyl-7-methylpterin and a third compound, named methaniline which was identified as 4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'----1')O-alpha -ribofuranosyl-5'-phosphoric acid]aniline, in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Methanosarcina barkeri contains a closely related coenzyme called sarcinapterin, which was identified as a L-glutamyl derivative of methanopterin, where the glutamate moiety is attached to the alpha-carboxylic acid group of the alpha-hydroxyglutaric acid moiety of methanopterin via an amide linkage.     

Purification and properties of malate dehydrogenase from the thermoacidophilic archaebacterium Thermoplasma acidophilum

Malate dehydrogenase from the thermoacidophilic archaebacterium Thermoplasma acidophilum is purified 50-fold to electrophoretic homogeneity. The purified enzyme crystallizes readily. Native malate dehydrogenase shows a relative molecular mass of 144 000. It is a tetramer of identical subunits with a relative molecular mass of 36 600. Malate dehydrogenase from Thermoplasma uses both NADH and NADPH as coenzyme to reduce oxaloacetate. The enzyme shows A-side (pro-R) stereospecificity for both coenzymes. The pH optimum for the reduction of oxaloacetate in the presence of NADH is found to be at pH 8.1. At pH 7.4 the Km value for oxaloacetate is found to be 5.6 microM while for NADH a value of 11.7 microM is found. The homogeneous enzyme shows a turnover number of kcat = 108 s-1.     

The enigmatic planctomycetes may hold a key to the origins of methanogenesis and methylotrophy

Methanogenesis and methane oxidation are the major biological processes affecting the global cycling of the powerful greenhouse gas methane. To carry out the two alternative bioconversions, Nature has cleverly recycled key reactions for the C1 transfers between the oxidation levels of formaldehyde and formate, and these involve analogous enzyme systems and common specialized cofactors, methanopterin and methanofuran. Until recently, the distribution of these functions has been limited to methanogenic archaea and methylotrophic proteobacteria, and their evolutionary history remained obscure. Single interdomain lateral transfer of the respective genes has been suggested to play a role. Here we show that genes for C1 transfer reactions linked to methanopterin and methanofuran are also present in diverse representatives of the enigmatic bacterial clade, the Planctomycetes. Phylogenetic analysis places the planctomycete sequences as distantly from their archaeal counterparts as from their proteobacterial counterparts, suggesting novel scenarios for the evolution of the C1 transfer functions in both methanogens and methylotrophs. This finding suggests a possible role for Planctomycetes in the evolution of the methane cycle on Earth.     

Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes

The hyperthermophilic euryarchaeon Methanococcus jannaschii uses coenzyme M (2-mercaptoethanesulfonic acid) as the terminal methyl carrier in methanogenesis. We describe an enzyme from that organism, (2R)-phospho-3-sulfolactate synthase (ComA), that catalyzes the first step in coenzyme M biosynthesis. ComA catalyzed the stereospecific Michael addition of sulfite to phosphoenolpyruvate over a broad range of temperature and pH conditions. Substrate and product analogs moderately inhibited activity. This enzyme has no significant sequence similarity to previously characterized enzymes; however, its Mg(2+)-dependent enzyme reaction mechanism may be analogous to one proposed for enolase. A diverse group of microbes and plants have homologs of ComA that could have been recruited for sulfolactate or sulfolipid biosyntheses.     

Intermediary carbohydrate metabolism in the adult filarial worm Setaria digitata.

Several key enzymes related to carbohydrate metabolism were assayed in Setaria digitata. In the cytosolic fraction pyruvate kinase, phosphoenolpyruvate carboxykinase, malate dehydrogenase, malic enzyme, aspartate transaminase and alanine transaminase were found. Among the TCA cycle enzymes succinate dehydrogenase, fumarate reductase, fumarase (malate dehydration), malate dehydrogenase (malate oxidation and oxaloacetate reduction) and malic enzyme (malate decarboxylation) were detected in the mitochondrial fraction. Only reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase, NADH oxidase and NADH-cytochrome c reductase were found in the mitochondrial fraction. The significance of these results with respect to the metabolic capabilities of the worm are discussed.     

Determination of NAD Malic Enzyme in Leaves of C(4) Plants : EFFECTS OF MALATE DEHYDROGENASE AND OTHER FACTORS

Malate dehydrogenase may interfere with the assay of NAD malic enzyme, as NADH is formed during the conversion of malate to oxaloacetate. During the present study, two additional effects of malate dehydrogenase were investigated; they are evident only if the malate dehydrogenase reaction is allowed to reach equilibrium prior to initiating the malic enzyme reaction. One of these (Outlaw, Manchester 1980 Plant Physiol 65: 1136-1138) might cause an underestimation of NAD reduction by malic enzyme due to the oxidation of NADH during reversal of the malate dehydrogenase reaction. A second effect may result in overestimation of malic enzyme activity, as Mn²⁺-catalyzed oxaloacetate decarboxylation causes continuing net NADH formation via malate dehydrogenase. These effects were studied by assaying the activity of a partially purified preparation of Amaranthus retroflexus NAD malic enzyme in the presence or absence of purified NAD malate dehydrogenase.     

Molecular basis for the transfer of nicotinamide adenine dinucleotide among dehydrogenases

NADH is transferred directly from one dehydrogenase enzyme site to another without intervention of the aqueous solvent whenever the two dehydrogenases are of opposite chiral specificity as regards the C4 H of NADH which is transferred in the catalyzed reduction reaction. When both enzymes catalyze the transfer of hydrogen from the same face of the nicotinamide ring, direct enzyme-enzyme transfer of NADH is not possible [Srivastava, D. K., & Bernhard, S. A. (1984) Biochemistry 23, 4538-4545; Srivastava, D. K., & Bernhard, S. A. (1985) Biochemistry (preceding paper in this issue)]. Utilizing an advanced computer graphics facility, and the known three-dimensional coordinates for three dehydrogenases, we have investigated the feasibility of various aspects of the direct transfer of dinucleotide from the site of one enzyme to the site of the other. The facile passage of the coenzyme through the first enzyme site requires an open protein conformation, characteristic of the apoenzyme rather than the holoenzyme structure. Since two dehydrogenases of the same chirality bind coenzyme in the same conformation, the direct transfer of coenzyme from one site to the other is impossible due to the restriction in molecular rotation of the coenzyme in the path of transfer from one binding site to the other; therefore, coenzyme can only be transferred from one dehydrogenase site to another site via the intermediate dissociation of coenzyme into the aqueous milieu. In contrast, when an A dehydrogenase and a B dehydrogenase are juxtaposed, it is stereochemically feasible to transfer the nicotinamide ring from its specific binding site in one enzyme to the site in the other.(ABSTRACT TRUNCATED AT 250 WORDS)     

The first examples of (S)-2-hydroxyacid dehydrogenases catalyzing the transfer of the pro-4S hydrogen of NADH are found in the archaea.

Reduction of 2-oxoacids to the corresponding (S)-2-hydroxyacids is an important transformation in biochemistry. To date all (S)-2-hydroxyacid dehydrogenases belonging to the L-lactate/L-malate dehydrogenase family have been found to transfer the pro-4R hydrogen of either NADH or NADPH to C-2 of the 2-oxoacid substrates during their reduction. Here, we report that recombinantly generated (S)-2-hydroxyacid dehydrogenases present in the methanoarchaea Methanococcus jannaschii and Methanothermus fervidus use the pro-4S hydrogen of NADH to reduce a series of 2-oxoacids to the corresponding (S)-2-hydroxyacids. This information as well as the low sequence identity between these archaeal enzymes and the L-lactate/L-malate family of enzymes indicate that these enzymes are not evolutionary related and therefore constitute a new class of (S)-2-hydroxyacid dehydrogenases.     

The role of ubiquinone in the respiratory chain of Acetobacter xylinum

1. Whole cells of Acetobacter xylinum were found to contain a quinone of the ubiquinone (coenzyme Q) group. The quinone was isolated from the cells and crystallized. It was identified by its physical, chemical and spectroscopic properties as a ubiquinone with 10 isoprene units (ubiquinone-10). No naphthaquinone was detected in the cells. 2. Cell-free extracts prepared by means of a French pressure cell were separated into three fractions by differential centrifugation. The ubiquinone was located predominantly in the particulate fraction sedimenting at 33000g, which also contained most of the NADH oxidase and malate oxidase activities. The concentration of ubiquinone-10 in extracts was similar to that of the flavoproteins and about three times the concentration of the individual cytochromes. 3. Aerobic incubations of crude extracts with either NADH or malate resulted in reduction of the endogenous ubiquinone-10 to steady-state concentrations of 55 and 40% of the total quinone respectively. In the presence of cyanide more than 95% of the endogenous ubiquinone-10 was reduced by either NADH or malate. 4. The initial rate of reduction of endogenous ubiquinone-10 by malate and the rate of ubiquinol oxidation, in A. xylinum extracts, were found to be compatible with the overall rate of malate oxidation with oxygen. 5. The effects of various respiratory inhibitors on the oxidation-reduction reactions of the endogenous quinone indicate that its position on the respiratory chain is between the malate flavoprotein dehydrogenase and the cytochrome chain.     

Properties and biochemical characterization of NADH 5 alpha-reductase from rat liver microsomes

NADH 5 alpha-reductase is present in microsomes of various rat organs: heart and skeletal muscle, liver, adrenal glands, kidney, testes and prostate. The enzyme from rat liver microsomes utilizes B-hydrogen from the coenzyme NADH for steroid reduction. After solubilization of the enzyme with the nonionic detergent lubrol, phosphatidylcholine is necessary to restore the activity. This reactivation of the enzyme activity is paralleled by a corresponding increase of Vmax for testosterone (17 beta-hydroxy-4-androsten-3-one). Km and Vmax for testosterone change, Km and Vmax for the coenzyme NADH remain constant with an alteration of phosphate concentration in the incubation medium. The NADH 5 alpha-reductase is inhibited by numerous substances: amytal, phenobarbital, mepacrin, thenoyltrifluoracetone, gallic acid propyl ester, dicoumarol, pentachlorophenol, NADP and antibodies against rat liver NADPH ferrihemoprotein reductase. Antibodies against rat liver cytochrome-b5 reductase cause an activation of NADH 5 alpha-reductase.     

Expression of the Escherichia coli pntA and pntB genes, encoding nicotinamide nucleotide transhydrogenase, in Saccharomyces cerevisiae and its effect on product formation during anaerobic glucose fermentation.

We studied the physiological effect of the interconversion between the NAD(H) and NADP(H) coenzyme systems in recombinant Saccharomyces cerevisiae expressing the membrane-bound transhydrogenase from Escherichia coli. Our objective was to determine if the membrane-bound transhydrogenase could work in reoxidation of NADH to NAD+ in S. cerevisiae and thereby reduce glycerol formation during anaerobic fermentation. Membranes isolated from the recombinant strains exhibited reduction of 3-acetylpyridine-NAD+ by NADPH and by NADH in the presence of NADP+, which demonstrated that an active enzyme was present. Unlike the situation in E. coli, however, most of the transhydrogenase activity was not present in the yeast plasma membrane; rather, the enzyme appeared to remain localized in the membrane of the endoplasmic reticulum. During anaerobic glucose fermentation we observed an increase in the formation of 2-oxoglutarate, glycerol, and acetic acid in a strain expressing a high level of transhydrogenase, which indicated that increased NADPH consumption and NADH production occurred. The intracellular concentrations of NADH, NAD+, NADPH, and NADP+ were measured in cells expressing transhydrogenase. The reduction of the NADPH pool indicated that the transhydrogenase transferred reducing equivalents from NADPH to NAD+.     

Purification, characterization and identification of aromatic 2-oxo acid reductase.

Aromatic 2-oxo acid reductase was purified to homogeneity from the cytosol of dog heart. The purified enzyme utilized various 2-oxo acids as substrates in the following order of activity: oxaloacetate > 3,5-diiodo-4-hydroxyphenylpyruvate > indolepyruvate > phenylpyruvate. Little or no activity was detected with glyoxylate, pyruvate, hydroxypyruvate, 2-oxoglutarate and 2-oxoadipate. NADH was active as coenzyme but not NADPH. The enzyme has an isoelectric point of 5.4 and is probably composed of two identical subunits with a molecular weight of approx. 40000. Evidence was presented that aromatic 2-oxo acid reductase is identical with one of the cytosol malate dehydrogenase isoenzymes. The enzyme was also found in the brain, kidney and liver of dog.