Resolution of mitochondrial NADH dehydrogenase and isolation of two iron-sulfur proteins

The low molecular weight NADH dehydrogenase which can be solubilized from the mitochondrial NADH-ubiquinone oxidoreductase complex with chaotropic agents consists of three subunits in equimolar ratio [Galante, Y. M., & Hatefi, Y. (1979) Arch. Biochem. Biophys. 192, 559]. The largest subunit (subunit I) can be completely separated from the other two (subunits II + III) by treatment with sodium trichloroacetate and ammonium sulfate fractionation. Both the subunit I and subunit II + III fractions contain iron and acid-labile sulfur. From visible and EPR spectroscopy and the iron and acid-labile sulfide content, we propose that the subunit II + III fraction contains a binuclear cluster. The cluster structure present in subunit I is as yet unclear. On separation of the subunits of NADH dehydrogenase, the FMN is lost.     

Localization of retinoid binding proteins, retinoid receptors, and retinaldehyde dehydrogenase in the chick eye

Retinoids have many functions in the eye, including, perhaps, the visual guidance of ocular growth. Therefore, we identified where retinoid receptors, binding proteins, and biosynthetic enzymes are located in the ocular tissues of the chick as a step toward discovering where retinoids are generated and where they act. Using antibodies to interphotoreceptor retinoid binding protein (IRBP), cellular retinol binding protein (CRBP), cellular retinoic acid binding protein (CRABP), cellular retinaldehyde binding protein (CRALBP), retinaldehyde dehydrogenase (RALDH), and retinoic acid receptors (RAR and RXR), we localized these proteins to cells in the retina, retinal pigmented epithelium, choroid and sclera of the chick eye. IRBP was detected in the photoreceptor layer and pigmented epithelium; CRBP was in the pigmented epithelium; CRABP was in amacrine and bipolar cells in the retina; CRALBP was in Müller cells, pigmented epithelium, choroid, and fibrous sclera; RALDH was in retinal amacrine cells, pigmented epithelium, and choroid; RAR was in amacrine cells, choroid, and chondrocytes and fibroblasts in the sclera; and RXR was in amacrine and ganglion cells, bipolar cell nuclei, choroid, and chondrocytes. We also found that the growth-modulating toxins colchicine and quisqualate destroyed selectively different subsets of CRABP-containing amacrine cells. We conclude that the distribution of proteins involved in retinoid metabolism is consistent with a role of retinoids not only in phototransduction, but also in maintenance of cellular phenotype and visual guidance of ocular growth.     

Bacterial membrane proteins. Properties of Micrococcus lysodeikticus NADH dehydrogenase]

NADH dehydrogenase was isolated from M. lysodeikticus membranes with FAD as a prosthetic group. It was found the enzyme molecular weight is about 140000 in 0,01 M phosphate buffer, pH 7,4 in 1% Triton X-100. The enzyme molecules are dimers consisting of two subunits with molecular weight of 70000. The content of alpha-helical regions is 30%, that of beta-forms is 13%. The protein globule is cross-linked with the disulfide bonds and has hydrophobic regions on its surface.     

Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase

The Bacillus subtilis gltAB operon, encoding glutamate synthase, requires a specific positive regulator, GltC, for its expression and is repressed by the global regulatory protein TnrA. The factor that controls TnrA activity, a complex of glutamine synthetase and a feedback inhibitor, such as glutamine, is known, but the signal for modulation of GltC activity has remained elusive. GltC-dependent gltAB expression was drastically reduced when cells were grown in media containing arginine or ornithine or proline, all of which are inducers and substrates of the Roc catabolic pathway. Analysis of gltAB expression in mutants with various defects in the Roc pathway indicated that rocG-encoded glutamate dehydrogenase was required for such repression, suggesting that the substrates or products of this enzyme are the real effectors of GltC. Given that RocG is an enzyme of glutamate catabolism, the main regulatory role of GltC may be prevention of a futile cycle of glutamate synthesis and degradation in the presence of arginine-related amino acids or proline. In addition, high activity of glutamate dehydrogenase was incompatible with activity of TnrA.     

Formation of lactate dehydrogenase complexes with proteins and polyelectrolytes. A possible physiological role

The effect of polymers (proteins, polyaminoacids, polyethylenimine) on kinetic parameters of lactate dehydrogenase (LDH) from porcine skeletal muscle was studied. Activation of the enzyme which was partially due to the association of LDH dimers was observed. A hypothesis was proposed, according to which the contribution of dissociation of oligomeric enzymes in the regulation of their activity in vivo is negligible due to the equilibrium shift towards association in dissociable enzyme systems.     

The tissue-specific expression and developmental regulation of two nuclear genes encoding rat mitochondrial proteins. Medium chain acyl-CoA dehydrogenase and mitochondrial malate dehydrogenase

To study the regulation of nuclear genes which encode mitochondrial enzymes involved in oxidative metabolism, absolute levels of mRNA encoding rat medium chain acyl-CoA dehydrogenase (MCAD) and rat mitochondrial malate dehydrogenase (mMDH) were determined in developing and adult male rat tissues. MCAD mRNA is expressed in a variety of adult male tissues with highest steady state levels in heart, adrenal, and skeletal muscle and lowest levels in brain, lung, and testes. In comparison, steady state levels of mMDH mRNA in adult male rat tissues were similar to those of MCAD mRNA in heart, small intestine, adrenal, and skeletal muscle but markedly different in brain, stomach, and testes. Thus, the steady-state levels of MCAD and mMDH mRNA are highest in adult tissues with high energy requirements. Dot blot analysis of RNA prepared from late fetal, suckling, and weaning rat heart, liver, and brain demonstrated the presence of MCAD and mMDH mRNA during the fetal period in all three tissues. Both MCAD and mMDH mRNA levels increased 2-2.5-fold at birth followed by a decline during the first postnatal week in heart and liver. The patterns of accumulation of these mRNAs in heart and liver during the weaning and early adult periods were also similar, although the absolute levels were significantly different. Brain MCAD mRNA levels were consistently low (less than 0.1 pg/micrograms total cellular RNA) throughout the developmental stages. However, brain mMDH mRNA levels exhibited a marked increase during the weaning period, reaching a peak concentration which is higher than the level of mMDH mRNA in heart and liver at any point during development. These results indicate that the level of expression of the nuclear genes encoding MCAD and mMDH is tissue-specific and developmentally regulated. The patterns of MCAD and mMDH mRNA accumulation parallel the changes in energy metabolism which occur during development and among adult tissues.     

Three different proteins exhibiting NAD-dependent acetaldehyde dehydrogenase activity from Alcaligenes eutrophus

The existence of three different proteins exhibiting NAD-dependent acetaldehyde dehydrogenase activity was confirmed in Alicaligenes eutrophus. The fermentative alcohol dehydrogenase, which also exhibits acetaldehyde dehydrogenase activity, is one of these proteins. The other two proteins were purified from A. eutrophus N9A mutant AS4 grown on ethanol applying chromatography on DEAE-Sephacel and triazine-dye affinity media. Acetaldehyde dehydrogenase II, which amounts to about 14% of the total soluble protein in cells grown on ethanol, was purified to homogeneity. The relative molecular masses of the native enzyme and of the subunits were 195,000 or 56,000, respectively. This enzyme exhibits a high affinity for acetaldehyde (Km = 4 microM). Acetaldehyde dehydrogenase I amounts only to less than 1% of the total soluble protein. The relative molecular masses of the native enzyme and of the subunits were 185,000 and 52,000, respectively. This enzyme exhibits a low affinity for acetaldehyde (Km = 2.6 mM). Antibodies raised against acetaldehyde dehydrogenase II did not react with acetaldehyde dehydrogenase I. Two different strains, A. eutrophus N9A mutant AS1, which represents a different mutant type and can utilize both ethanol or 2,3-butanediol, and the type strain of A. eutrophus (TF93), which can utilize ethanol, form two acetaldehyde dehydrogenases during growth on ethanol, too. As in AS4, one of these enzymes from each strain amounted to a substantial portion of the total soluble protein in the cells. These major acetaldehyde dehydrogenases were purified from both strains; they resemble acetaldehyde dehydrogenase II isolated from AS4 in all relevant properties. Antibodies against the enzyme isolated from AS4 gave identical cross-reactions with the enzymes isolated from AS1 and TF93.     

Effect of pyruvate dehydrogenase coenzymes and mitochondrial proteins on the accumulation of [35S]lipoic acid

Coenzymes introduced in the ratio, peculiar for pyruvate dehydrogenase complex into the medium containing fresh-isolated mitochondria and oxidation substrate--pyruvate increase accumulation of [35S] lipoate by these organelles. This process is highly stimulated by introducing either the only CoA or a coenzyme mixture (CoA, thiamine pyrophosphate, FAD, NAD). Addition of phosphate-extracted components of mitochondria and their protein fraction with coenzymes in the ratio indicated above provides maximum accumulation of [35S] lipoate by liver mitochondria. An equimolar mixture of coenzymes as well as protein components evoke no reliable variations in [35S] lipoate accumulation by albino rat liver mitochondria, while addition of the only thiamine pyrophosphate decreases this accumulation. Reconstruction of multienzyme complexes of coenzymes and apoenzymes on mitochondrion membranes accounts for the results obtained.     

Identification of proteins interacting with lactate dehydrogenase in claw muscle of the porcelain crab Petrolisthes cinctipes

Biochemical adaptation of enzymes involves conservation of activity, stability and affinity across a wide range of intracellular and environmental conditions. Enzyme adaptation by alteration of primary structure is well known, but the roles of protein–protein interactions in enzyme adaptation are less well understood. Interspecific differences in thermal stability of lactate dehydrogenase (LDH) in porcelain crabs (genus Petrolisthes) are related to intrinsic differences among LDH molecules and by interactions with other stabilizing proteins. Here, we identified proteins that interact with LDH in porcelain crab claw muscle tissue using co-immunoprecipitation, and showed LDH exists in high molecular weight complexes using size exclusion chromatography and Western blot analyses. Co-immunoprecipitated proteins were separated using 2D SDS PAGE and analyzed by LC/ESI using peptide MS/MS. Peptide MS/MS ions were compared to an EST database for Petrolisthes cinctipes to identify proteins. Identified proteins included cytoskeletal elements, glycolytic enzymes, a phosphagen kinase, and the respiratory protein hemocyanin. Our results support the hypothesis that LDH interacts with glycolytic enzymes in a metabolon structured by cytoskeletal elements that may also include the enzyme for transfer of the adenylate charge in glycolytically produced ATP. Those interactions may play specific roles in biochemical adaptation of glycolytic enzymes.     

Expression and purification of His-tagged rat mitochondrial medium-chain acyl-CoA dehydrogenase wild-type and Arg256 mutant proteins

Mitochondrial medium-chain acyl-CoA dehydrogenase is a key enzyme for the beta-oxidation of fatty acids, and the deficiency of this enzyme in patient has been previously reported. We cloned the gene of rat mitochondrial medium-chain acyl-CoA dehydrogenase into a bacterial expression vector pLM1 with six continuous histidine codons attached to the 3' of the gene. The cloned gene was overexpressed in Escherichia coli and the soluble protein was purified with a nickel Hi-Trap chelating metal affinity column in 88% yield to apparent homogeneity. The specific activity of the purified His-tagged rat mitochondrial medium-chain acyl-CoA dehydrogenase was 4.0 U/mg. Arg256 is a highly conserved amino acid, which may play an important role in enzymatic reaction based on the crystal structure of medium-chain acyl-CoA dehydrogenase. We constructed four mutant expression plasmids of the enzyme using site-directed mutagenesis. Mutant proteins were overexpressed in E. coli and purified with a nickel metal affinity column. Kinetic studies of wild-type and mutant proteins were carried out, and the result confirmed that Arg256 is a very important residue of rat mitochondrial medium-chain acyl-CoA dehydrogenase. Our overexpression in E. coli and one-step purification of the highly active rat mitochondrial medium-chain acyl-CoA dehydrogenase greatly facilitated our further investigation of this enzyme, and our result from site-directed mutagenesis increased our understanding of medium-chain acyl-CoA dehydrogenase.     

Isolation from pig lens of two proteins with dihydrodiol dehydrogenase and aldehyde reductase activities.

Dimeric and monomeric proteins containing dihydrodiol dehydrogenase and aldehyde reductase activities were purified from pig lens. The dimeric enzyme of Mr 65,000 specifically oxidized the trans-dihydrodiols of naphthalene and benzene with NADP+ as a strict cofactor, and reduced alpha-diketones, aromatic aldehydes and glyceraldehyde with NADPH as a cofactor. The monomeric enzyme of Mr 35,000, although identical with aldose reductase, oxidized the trans-dihydrodiol of naphthalene at a pH optimum of 7.6. These results suggest that the two enzymes are involved in the pathogenesis of naphthalene cataract.     

Possibilities of biochemical taxonomy of bats using hemoglobin,lactate dehydrogenase,esterases and other proteins

• 1.1. Bat hemoglobin resembles other mammalian Hb's in its physiological properties, and Hb differences among bat species are minor.
• 2.2. One polymorphism of the H chain of lactate dehydrogenase occurs in Myotis lucifugus and M. keenii, and another occurs in Eptesicus fuscus. Bat heart and muscle have identical LDH isozyme profiles.
• 3.3. Esterases and major low ionic strength extractabe proteins show a number of differences at the generic level, as well as some polymorphisms which cross species lines.
• 4.4. The protein studies indicate that bats have great individual variation, often of a type comparable to known genetically based protein polymorphisms in other species, but apparently have not had time to accumulate extensive divergent species specificity.

     

Expression and purification of His-tagged rat mitochondrial short-chain 3-hydroxyacyl-CoA dehydrogenase wild-type and Ser137 mutant proteins

Mitochondrial 3-hydroxyacyl-CoA dehydrogenase is a key enzyme in the beta-oxidation of fatty acids. The deficiency of this enzyme in patients has been previously reported. We cloned the gene of rat mitochondrial 3-hydroxyacyl-CoA dehydrogenase in a bacterial expression vector pLM1 with six continuous histidine codons attached to the 5' of the gene. The cloned gene was overexpressed in Escherichia coli and the soluble protein was purified with a nickel HiTrap chelating metal affinity column to apparent homogeneity. The specific activity of the purified His-tagged rat mitochondrial 3-hydroxyacyl-CoA dehydrogenase was 452 U/mg. Ser137 is a highly conserved amino acid, which, it has been suggested, is an important residue because of its proximity to the modeled L-3-hydroxyacyl-CoA substrate in the crystal structure of 3-hydroxyacyl-CoA dehydrogenase. We constructed three mutant expression plasmids of the enzyme using site-directed mutagenesis. Mutant proteins were overexpressed in E. coli and purified with a nickel metal affinity column. Kinetic studies of wild-type and mutant proteins were carried out, and the result confirmed that Ser137 is a very important residue of rat mitochondrial 3-hydroxyacyl-CoA dehydrogenase. Our overexpression in E. coli and one-step purification of the highly active rat mitochondrial 3-hydroxyacyl-CoA dehydrogenase greatly facilitated our further investigation of this enzyme, and our result from site-directed mutagenesis increased our understanding of 3-hydroxyacyl-CoA dehydrogenase.     

Covalent binding of proteins and glucose-6-phosphate dehydrogenase to cellulosic carriers activated with s-triazine trichloride

A method was developed for covalently binding proteins and enzymes to cellulosic carriers such that the enzymes retained high specific activity. Optimal conditions for activating the carriers with s-triazine trichloride were found to be: (a) pretreatment of cellulose with 3 m NaOH; and (b) reaction with 5% ($\text{w}\text{w}$) s-triazine trichloride in dioxane-xylene (1:1 $\text{w}\text{w}$) for 30 min at room temperature. All proteins tested bound most readily at pH values below pH 7. Extensive investigation of immobilized glucose-6-phosphate dehydrogenase showed that: (a) over 80% of the specific activity of the enzyme was retained; and (b) the pH optimum and K_m values were not altered significantly from that of the free enzyme. The binding method has been applied successfully to hexokinase, phosphorylase and pronase.     

Targeting proteins to the lumen of endoplasmic reticulum using N-terminal domains of 11beta-hydroxysteroid dehydrogenase and the 50-kDa esterase.

Previous studies identified two intrinsic endoplasmic reticulum (ER) proteins, 11beta-hydroxysteroid dehydrogenase, isozyme 1 (11beta-HSD) and the 50-kDa esterase (E3), sharing some amino acid sequence motifs in their N-terminal transmembrane (TM) domains. Both are type II membrane proteins with the C terminus projecting into the lumen of the ER. This finding implied that the N-terminal TM domains of 11beta-HSD and E3 may constitute a lumenal targeting signal (LTS). To investigate this hypothesis we created chimeric fusions using the putative targeting sequences and the reporter gene, Aequorea victoria green fluorescent protein. Transfected COS cells expressing LTS-green fluorescent protein chimeras were examined by fluorescent microscopy and electron microscopic immunogold labeling. The orientation of expressed chimeras was established by immunocytofluorescent staining of selectively permeabilized COS cells. In addition, protease protection assays of membranes in the presence and absence of detergents was used to confirm lumenal or the cytosolic orientation of the constructed chimeras. To investigate the general applicability of the proposed LTS, we fused the N terminus of E3 to the N terminus of the NADH-cytochrome b5 reductase lacking the myristoyl group and N-terminal 30-residue membrane anchor. The orientation of the cytochrome b5 reductase was reversed, from cytosolic to lumenal projection of the active domain. These observations establish that an amino acid sequence consisting of short basic or neutral residues at the N terminus, followed by a specific array of hydrophobic residues terminating with acidic residues, is sufficient for lumenal targeting of single-pass proteins that are structurally and functionally unrelated.