NADP+-specific isocitrate dehydrogenase of Escherichia coli. II. Subunit structure

NADP+ -dependent isocitrate dehydrogenase isozymes from a psychrotrophic bacterium, Psychrobacter sp. strain 13A

The genes encoding dimeric and monomeric isocitrate dehydrogenase (IDH) isozymes from a psychrotrophic bacterium, strain 13A (13AIDH-D and 13AIDH-M, respectively), were cloned and sequenced. The deduced amino acid sequences of these two IDHs showed high degrees of identity with those of bacteria of genus Psychrobacter. Analysis of the 16S ribosomal RNA gene of the strain 13A revealed that this bacterium is classified to genus Psychrobacter. The optimum temperatures for activities of 13AIDH-D and 13AIDH-M were 55°C and 45°C, respectively, indicating that they are mesophilic. On the contrary, 13AIDH-D maintained 90% of its maximum activity after incubation for 10 min at 50°C, while the 13AIDH-M activity was completely lost under the same condition. In addition, 13AIDH-D showed much higher specific activity than 13AIDH-M. From northern and western blot analyses, the 13AIDH-D gene was found to be not transcribed under the growth conditions tested in this study. However, the catalytic ability of the mesophilic 13AIDH-M was concluded to be enough to sustain the growth of strain 13A at low temperatures. Therefore, a novel pattern of the contribution of IDH isozymes in cold-living bacteria to their growth at low temperatures was confirmed in strain 13A.

Analysis of amino acid residues involved in the thermal properties of isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia maris, and a psychrotrophic bacterium, Pseudomonas psychrophila

Monomeric NADP⁺-dependent isocitrate dehydrogenase (IDH) from a psychrophilic bacterium, Colwella maris, (CmIDH) is a cold-adapted enzyme, whereas that of a psychrotrophic bacterium, Pseudomonas psychrophila, (PpIDH) is mesophilic. However, the amino acid sequence identity of the two IDHs is high (67%). To identify the amino acid residues involved in the differences in their thermal properties, such as optimum temperature and thermostability for activity, six amino acid residues located in the corresponding positions of their regions 2 and 3 were substituted by site-directed mutagenesis, and several thermal properties of the mutated IDHs were examined. CmIDH mutants, CmE538L, CmE596L and CmA741S, substituted at Glu538, Glu596 and Ala741 by the corresponding PpIDH residues of Leu, Leu and Ser, respectively, exhibited higher thermostability than wild-type CmIDH (CmWT). Furthermore, the specific activity of CmE596L and CmA741S was higher than that of CmWT. On the other hand, the corresponding mutants of PpIDH PpL536E, PpL594E and PpS739A were more thermolabile than wild-type PpIDH, and PpL594E had a lower specific activity at temperatures over 45°C. These results suggested that these amino acid residues of CmIDH and PpIDH are involved in their thermal properties.

Effects of the substituted amino acid residues on the thermal properties of monomeric isocitrate dehydrogenases from a psychrophilic bacterium, Psychromonas marina, and a mesophilic bacterium, Azotobacter vinelandii

A cold-adapted monomeric isocitrate dehydrogenase from a psychrophilic bacterium, Psychromonas marina (PmIDH), showed a high degree of amino acid sequential identity (64%) to a mesophilic one from a mesophilic bacterium, Azotobacter vinelandii (AvIDH). In this study, eight corresponding amino acid residues were substituted between them by site-directed mutagenesis, and several thermal properties of the mutated IDHs were examined. In the PmIDH mutants, PmL735F, substituted Leu735 of PmIDH by the corresponding Phe of AvIDH, showed higher specific activity and thermostability of activity than wild-type PmIDH, while the H600Y and N741P mutations of PmIDH resulted in decreased specific activity and thermostability of activity. On the other hand, among the AvIDH mutants, AvP718T showed lower optimum temperature and thermostability of activity than wild-type AvIDH. In PmIDH variously combined the H600Y, L735F and N741P mutations, PmH600YL735F, including the H600Y and L735F mutations, showed higher specific activity than PmH600Y and similar optimum temperature and thermostability of activity to PmH600Y. Furthermore, PmL735FN741P exhibited higher specific activity and thermostability of activity than PmN741P. These results indicated that the effects of the three mutations of PmIDH are additive on the specific activity of both PmH600YL735F and PmL735FN741P and on thermostability of PmL735FN741P.

Contribution of Three Different Regions of Isocitrate Dehydrogenases from Psychrophilic and Psychrotolerant Bacteria to Their Thermal Properties

Monomeric isocitrate dehydrogenases of a psychrophilic bacterium, Colwellia maris, and a psychrotolerant bacterium, Pseudomonas psychrophila, (CmIDH and PpIDH) are cold-adapted and mesophilic, respectively. On the other hand, previous studies revealed that the monomeric IDH of Azotobacter vinelandii (AvIDH) is also mesophilic and the regions 2 and 3 among three regions of this enzyme are involved in the thermal properties. Therefore, to examine whether the region(s) responsible for the mesophilic properties are common between PpIDH and AvIDH, the genes of chimeric IDHs exchanging three regions of PpIDH and CmIDH in various combinations were constructed and overexpressed as His-tagged recombinant proteins in the Escherichia coli cells, and the chimeric and wild-type PpIDH and CmIDH were purified with Ni-chelating affinity column chromatography. The swapping chimeras of the regions 2 or 3 in PpIDH and CmIDH showed lower and higher optimum temperatures for activities and their thermostabilities than the wild-type ones, respectively. On the other hand, the exchange of the respective region 1 hardly influenced these properties of the two IDHs. Therefore, the regions 2 and 3 of the two IDHs were confirmed to be involved in their thermal properties. These results were coincident with those of the previous study on chimeric IDHs between AvIDH and CmIDH, indicating that the common regions of AvIDH and PpIDH are responsible for their mesophilic properties and the amino acid residues involved in their thermal properties are present in the regions 2 and 3.

NADP+-dependent isocitrate dehydrogenase from a psychrophilic bacterium, Psychromonas marina

The gene encoding NADP⁺-dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) of a psychrophilic bacterium, Psychromonas marina, was cloned and sequenced. The open reading frame of the gene encoding IDH of P. marina (PmIDH) was 2229 bp in length and corresponded to a polypeptide composed of 742 amino acids. The molecular mass of IDH was calculated as 80,426 Da. The deduced amino acid sequence of PmIDH exhibited high degrees of homology with the monomeric IDH from other bacteria such as Colwellia maris (62% identity) and Azotobacter vinelandii (AvIDH) (64%). His-tagged PmIDH overexpressed in Escherichia coli cells was purified and characterized. The optimum temperature of PmIDH activity was about 35 °C; however, the enzyme lost 74% of the activity after incubation for 10 min at 30 °C, indicating that this enzyme is thermolabile. Chimeric enzymes produced through domain swapping between PmIDH and mesophilic AvIDH were constructed and their optimum temperatures and thermostability were determined. The results suggest that regions 2 and 3, especially region 3, of the two IDHs are involved in their catalytic activities and optimum temperature and thermostability for activity.

Characterization of NADP(+)-dependent isocitrate dehydrogenase isozymes from a psychrophilic bacterium, Colwellia psychrerythraea strain 34H

NADP(+)-dependent isocitrate dehydrogenase (IDH) isozymes of a psychrophilic bacterium, Colwellia psychrerythraea strain 34H, were characterized. The coexistence of monomeric and homodimeric IDHs in this bacterium was confirmed by Western blot analysis, the genes encoding two monomeric (IDH-IIa and IDH-IIb) and one dimeric (IDH-I) IDHs were cloned and overexpressed in Escherichia coli, and the three IDH proteins were purified. Both of the purified IDH-IIa and IDH-IIb were found to be cold-adapted enzymes while the purified IDH-I showed mesophilic properties. However, the specific activities of IDH-IIa and IDH-IIb were lower even at low temperatures than that of IDH-I. Therefore, IDH-I was suggested to be important for the growth of this bacterium. The results of colony formation of E. coli transformants carrying the respective IDH genes and IDH activities in their crude extracts indicated that the expression of the IDH-IIa gene is cold-inducible in the E. coli cells.

Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide

Biochemical network reconstructions have become popular tools in systems biology. Metabolicnetwork reconstructions are biochemically, genetically, and genomically (BiGG) structured databases of biochemical reactions and metabolites. They contain information such as exact reaction stoichiometry, reaction reversibility, and the relationships between genes, proteins, and reactions. Network reconstructions have been used extensively to study the phenotypic behavior of wild-type and mutant stains under a variety of conditions, linking genotypes with phenotypes. Such phenotypic simulations have allowed for the prediction of growth after genetic manipulations, prediction of growth phenotypes after adaptive evolution, and prediction of essential genes. Additionally, because network reconstructions are organism specific, they can be used to understand differences between organisms of species in a functional context.There are different types of reconstructions representing various types of biological networks (metabolic, regulatory, transcription/translation). This chapter serves as an introduction to metabolic and regulatory network reconstructions and models and gives a complete description of the core Escherichia coli metabolic model. This model can be analyzed in any computational format (such as MATLAB or Mathematica) based on the information given in this chapter. The core E. coli model is a small-scale model that can be used for educational purposes. It is meant to be used by senior undergraduate and first-year graduate students learning about constraint-based modeling and systems biology. This model has enough reactions and pathways to enable interesting and insightful calculations, but it is also simple enough that the results of such calculations can be understoodeasily.

Production of gamma-aminobutyric acid from glucose by introduction of synthetic scaffolds between isocitrate dehydrogenase, glutamate synthase and glutamate decarboxylase in recombinant Escherichia coli

Escherichia coli were engineered for the direct production of gamma-aminobutyric acid from glucose by introduction of synthetic protein scaffold. In this study, three enzymes consisting GABA pathway (isocitrate dehydrogenase, glutamate synthase and glutamate decarboxylase) were connected via synthetic protein scaffold. By introduction of scaffold, 0.92g/L of GABA was produced from 10g/L of glucose while no GABA was produced in wild type E. coli. The optimum pH and temperature for GABA production were 4.5 and 30°C, respectively. When competing metabolic network was inactivated by knockout mutation, maximum GABA concentration of 1.3g/L was obtained from 10g/L glucose. The recombinant E. coli strain which produces GABA directly from glucose was successfully constructed by introduction of protein scaffold.

Marker genes for the metabolic adaptation of Pseudomonas aeruginosa to the hypoxic cystic fibrosis lung environment

Pseudomonas aeruginosa is the leading pathogen of chronic cystic fibrosis (CF) lung infection. Life-long persistence in the inflamed and ever fluctuating CF lungs results in the selection of a variety of changes in P. aeruginosa physiology. Accumulating evidence suggests that especially metabolic changes support the survival and growth of P. aeruginosa within the hypoxic and nutritious CF mucus. To investigate if metabolic adaptations we described for hypermutable P. aeruginosa from late CF lung disease (Hoboth et al., 2009. J. Infect. Dis., pp. 118-130) may represent specific changes in response to the selective conditions within the oxygen-restricted CF mucus, we determined the expression of a set of genes during aerobic and hypoxic growth in LB and the artificial sputum medium ASM. We further focused on the regulation of the two isocitrate dehydrogenases Icd and Idh. Interestingly, both isoenzymes may replace each other under aerobic and hypoxic conditions. The NADPH- and RpoS-dependent Icd seems to be the leading isoenzyme under prolonged oxygen limitation and stationary growth phase. LacZ reporter analysis revealed that oxygen-restriction increased the expression levels of azu, cbb3-1, cbb3-2, ccpR, icd, idh and oprF gene, whereas himD and nuoA are increasingly expressed only during hypoxic growth in ASM. Overexpression of the anaerobic regulator Anr improved the expression of azu, ccpR, cbb3-2 and icd. In summary, expression of azu, cbb3-1, cbb3-2, ccpR, icd, idh, oprF, himD, and nuoA appeared to be beneficial for the growth of P. aeruginosa under hypoxic conditions indicating these genes may represent marker genes for the metabolic adaptation to the CF lung environment.

Analysis of amino acid residues involved in cold activity of monomeric isocitrate dehydrogenase from psychrophilic bacteria, Colwellia maris and Colwellia psychrerythraea

Monomeric isocitrate dehydrogenases from psychrophilic bacteria, Colwellia maris and Colwellia psychrerythraea (CmIDH-II and CpIDH-M, respectively) are cold-adapted enzymes and show a high degree of amino acid sequential identity to each other (77%). However, maximum activity of CpIDH-M at optimum temperature is much less than that of CmIDH-II. In the C-terminal region 3 of these enzymes, which was suggested from previous study to be responsible for their distinct catalytic ability, several sequential differences of amino acid residue are present. Among them, ten amino acid residues were exchanged between them by site-directed mutagenesis and several properties of the mutated enzymes were examined in this study. The mutated enzymes of CmIDH-II substituted its Gln671, Leu724 and Phe735 residues with the corresponding residues of CpIDH-M (termed Q671K, L724Q and F735L, respectively) showed lower specific activity and thermostability for activity than the wild-type enzyme. Furthermore, the decreased specific activity was also observed in L693F. In contrast, the corresponding mutants of CpIDH-M, F693L, Q724L and L735F, showed the increased specific activity and thermostability for activity. The catalytic efficiency (k(cat)/K(m)) values of these mutated CmIDH-II and CpIDH-M were lower and higher than those of their wild-type IDHs, respectively. These results suggest that the Gln671, Leu693, Leu724 and Phe735 residues of CmIDH-II are important for exerting its high catalytic ability.

Isocitrate dehydrogenase isozymes from a psychrotrophic bacterium, Pseudomonas psychrophila

The genes encoding monomer- and dimer-type isocitrate dehydrogenase (IDH) isozymes from a psychrotrophic bacterium, Pseudomonas psychrophila, were cloned and sequenced. Open reading frames of the genes were 2,226 and 1,257 bp in length and corresponded to polypeptides composed of 741 and 418 amino acids, respectively. The deduced amino acid sequences showed high sequence identity with those of psychrophilic bacteria, Colwellia maris and Colwellia psychrerythraea, (about 70% identity) and the respective types of the putative IDH genes from other bacteria of genus Pseudomonas (more than 80% identity). The two genes were located in opposite direction from each other with a spacer of 463 bases in the order of dimeric and monomeric IDH genes on the chromosomal DNA, but analyses of northern blotting and 5'-terminal regions of the mRNAs revealed that they are transcribed independently. The expression of monomer- and dimer-type IDH genes in C. maris are known to be cold- and acetate-inducible, respectively, while only slight inductions by low temperature and/or acetate were observed in the expression of the P. psychrophila monomer- and dimer-type IDH genes. Both of these IDH isozymes overproduced in Escherichia coli showed mesophilic properties, in contrast with monomer- and dimer-type IDHs of C. maris as cold adapted and mesophilic enzymes, respectively. The substitution of Glu55 residue in the P. psychrophila monomeric IDH for Lys, which is the corresponding residue conserved between the cold-adapted monomeric IDHs from C. maris and C. psychrerythraea, by site-directed mutagenesis resulted in the decreased thermostability and the lowered optimum temperature of activity, suggesting that this residue is involved in the mesophilic properties of the P. psychrophila monomeric IDH.

Disulfide bond formation in yeast NAD+-specific isocitrate dehydrogenase

The tricarboxylic acid cycle NAD+-specific isocitrate dehydrogenase (IDH) of Saccharomyces cerevisiae is an octameric enzyme composed of four heterodimers of regulatory IDH1 and catalytic IDH2 subunits. Recent structural analyses revealed the close proximity of Cys-150 residues from IDH2 in adjacent heterodimers, and features of the structure for the ligand-free enzyme suggested that formation of a disulfide bond between these residues might stabilize an inactive form of the enzyme. We constructed two mutant forms of IDH, one containing a C150S substitution in IDH2 and the other containing C56S/C242S substitutions in IDH2 leaving Cys-150 as the sole cysteine residue. Treatment of the affinity-purified enzymes with diamide resulted in the formation of disulfide bonds and in decreased activities for the wild-type and C56S/C242S enzymes. Both effects were reversible by the addition of dithiothreitol. Diamide had no effect on the C150S mutant enzyme, suggesting that Cys-150 is essential for the formation of a disulfide bond that inhibits IDH activity. Diamide-induced formation of the Cys-150 disulfide bond was also observed in vivo for yeast transformants expressing the wild-type or C56S/C242S enzymes but not for a transformant expressing the C150S enzyme. Finally, natural formation of the Cys-150 disulfide bond with a concomitant decrease in cellular IDH activity was observed during the stationary phase for the parental strain and for transformants expressing wild-type or C56S/C242S enzymes but not for a transformant expressing the C150S enzyme. A reduction in viability for the latter strain suggests that a decrease in IDH activity is important for metabolic changes in stationary phase cells.

Two isocitrate dehydrogenases from a psychrophilic bacterium, Colwellia psychrerythraea

Two structurally different monomeric and dimeric types of isocitrate dehydrogenase (IDH; EC 1.1.1.42) isozymes were confirmed to exist in a psychrophilic bacterium, Colwellia psychrerythraea, by Western blot analysis and the genes encoding them were cloned and sequenced. Open reading frames of the genes (icd-M and icd-D) encoding the monomeric and dimeric IDHs of this bacterium, IDH-M and IDH-D, were 2,232 and 1,251 bp in length and corresponded to polypeptides composed of 743 and 416 amino acids, respectively. The deduced amino acid sequences of the IDH-M and IDH-D showed high homology with those of monomeric and dimeric IDHs from other bacteria, respectively. Although the two genes were located in tandem, icd-M then icd-D, on the chromosomal DNA, a Northern blot analysis and primer extension experiment revealed that they are transcribed independent of each other. The expression of the monomeric and dimeric IDH isozyme genes in C. maris, a psychrophilic bacterium of the same genus as C. psychrerythraea, is known to be induced by low temperature and acetate, respectively, but no such induction in the expression of the C. psychrerythraea icd-M and icd-D genes was detected. IDH-M and IDH-D overexpressed in Escherichia coli were purified and characterized. In C. psychrerythraea, the IDH-M isozyme is cold-active whereas IDH-D is mesophilic, which is similar to C. maris that contains both cold-adapted and mesophilic isozymes of IDH. Experiments with chimeric enzymes between the cold-adapted monomeric IDHs of C. psychrerythraea and C. maris (IDH-M and ICD-II, respectively) suggested that the C-terminal region of the C. maris IDH-II is involved in its catalytic activity.

Purification and Some Properties of Isocitrate Dehydrogenase fromParacoccus denitrificans

NADP-dependent isocitrate dehydrogenase (ICDH) from the bacterium Paracoccus denitrificans was purified to homogeneity. The purification procedure involved ammonium sulphate fractionation, ion exchange chromatography, and gel permeation chromatography. The specific activity of purified ICDH was 801 nkat/mg, the yield of the enzyme 58%. The purity of the enzyme was checked by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulphate. ICDH is a dimer composed of two probably identical subunits of relative molecular weight 90,000. The pH optimum of the enzyme reaction in the direction of substrate oxidation was found to be 5.6; the presence of Mn2+ is essential for enzyme activity. The absorption and fluorescence spectra of the homogeneous enzyme were measured as well.

Isocitrate binding at two functionally distinct sites in yeast NAD+-specific isocitrate dehydrogenase

Yeast NAD(+)-specific isocitrate dehydrogenase (IDH) is an octamer containing two types of homologous subunits. Ligand-binding analyses were conducted to examine effects of residue changes in putative catalytic and regulatory isocitrate-binding sites respectively contained in IDH2 and IDH1 subunits. Replacement of homologous serine residues in either subunit site, S98A in IDH2 or S92A in IDH1, was found to reduce by half the total number of holoenzyme isocitrate-binding sites, confirming a correlation between detrimental effects on isocitrate binding and respective kinetic defects in catalysis and allosteric activation by AMP. Replacement of both serine residues eliminates isocitrate binding and measurable catalytic activity. The putative isocitrate-binding sites of IDH1 and IDH2 contain five identical and four nonidentical residues. Reciprocal replacement of the four nonidentical residues in either or both subunits (A108R, F136Y, T241D, and N245D in IDH1 and/or R114A, Y142F, D248T, and D252N in IDH2) was found to be permissive for isocitrate binding. This provides further evidence for two types of binding sites in IDH, although the authentic residues have been shown to be necessary for normal kinetic contributions. Finally, the mutant enzymes with residue replacements in the IDH1 site were found to be unable to bind AMP, suggesting that allosteric activation is dependent both upon binding of isocitrate at the IDH1 site and upon the changes in the enzyme normally elicited by this binding.

Regulation of acetate metabolism by protein phosphorylation in enteric bacteria

Growth of enteric bacteria on acetate as the sole source of carbon and energy requires operation of a particular anaplerotic pathway known as the glyoxylate bypass. In this pathway, two specific enzymes, isocitrate lyase and malate synthase, are activated to divert isocitrate from the tricarboxylic acid cycle and prevent the quantitative loss of acetate carbons as carbon dioxide. Bacteria are thus supplied with the metabolic intermediates they need for synthesizing their cellular components. The channeling of isocitrate through the glyoxylate bypass is regulated via the phosphorylation/dephosphorylation of isocitrate dehydrogenase, the enzyme of the tricarboxylic acid cycle which competes for a common substrate with isocitrate lyase. When bacteria are grown on acetate, isocitrate dehydrogenase is phosphorylated and, concomitantly, its activity declines drastically. Conversely, when cells are cultured on a preferred carbon source, such as glucose, the enzyme is dephosphorylated and recovers full activity. Such reversible phosphorylation is mediated by an unusual bifunctional enzyme, isocitrate dehydrogenase kinase/phosphatase, which contains both modifying and demodifying activities on the same polypeptide. The genes coding for malate synthase, isocitrate lyase, and isocitrate dehydrogenase kinase/phosphatase are located in the same operon. Their expression is controlled by a complex dual mechanism that involves several transcriptional repressors and activators. Recent developments have brought new insights into the nature and mode of action of these different regulators. Also, significant advances have been made lately in our understanding of the control of enzyme activity by reversible phosphorylation. In general, analyzing the physiological behavior of bacteria on acetate provides a valuable approach for deciphering at the molecular level the mechanisms of cell adaptation to the environment.

Purification and characterization of isocitrate dehydrogenase from a hyperthermophilic archaebacterium, Caldococcus noboribetus

Isocitrate dehydrogenase from a hyperthermophilic archaebacterium Caldococcus noboribetus produced in Escherichia coli was purified. The purification was performed by heat treatment at 80 degrees C followed by single column chromatography. N-terminal amino acid sequencing analysis revealed that the N-terminal methionine is removed from the purified enzyme. Gel filtration analysis suggests that the enzyme has a homodimeric structure with a molecular weight of 90,000. The isoelectric point of the enzyme was estimated to be 5.6 by isoelectric focusing electrophoresis. The circular dichroism spectrum suggests that the enzyme has a secondary structure consisting of 23% alpha-helix and 34% beta-sheet. Enzymatic activity was observed under neutral pH, and the highest specific activity was obtained using cacodylic acid-KOH (pH 7.0) buffer. MgCl2 or MnCl2 was essential for the activity, and KCl concentrations higher than 0.33 M had an inhibitory effect on it. Apparent Km values were 72 and 43 microM for D,L-isocitrate and NADP, respectively. The enzyme showed extremely high stability against heat treatment, and no activity loss was observed by the treatment at 80 degrees C. The specific activity of the enzyme increased as temperature rose. Nearly no activity was observed at 40 degrees C or lower.

Expression and gene disruption analysis of the isocitrate dehydrogenase family in yeast

Mammalian and yeast cells contain three isozymes of isocitrate dehydrogenase: mitochondrial NAD- and NADP-specific enzymes and a cytosolic NADP-specific enzyme. Independent metabolic functions of these enzymes in Saccharomyces cerevisiae were examined by analyses of expression and of phenotypes displayed by mutants containing all possible combinations of isozyme gene disruptions. All three isocitrate dehydrogenases are expressed at high levels with growth on nonfermentable carbon sources, whereas the mitochondrial NADP-specific enzyme constitutes the major cellular activity with growth on glucose. Distinct growth phenotypes are observed for mutants expressing a single isozyme, and expression of at least one isozyme is necessary for glutamate-independent growth. The NADP-specific tricarboxylic acid cycle isocitrate dehydrogenase from Escherichia coli was expressed in mitochondrial and cytosolic compartments of the yeast disruption mutants using plasmids carrying gene fusions of yeast promoters and a mitochondrial targeting presequence with the bacterial coding sequence. The bacterial enzyme is competent for restoration of NADP-specific functions in either compartment but does not compensate for function of the yeast NAD-specific tricarboxylic acid cycle enzyme.

Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1

The genes coding for two structurally different isocitrate dehydrogenase isozymes (IDH-I and IDH-II) of a psychrophilic bacterium, Vibrio sp. strain ABE-1, were cloned and sequenced. Open reading frames of the genes (icdI and icdII) are 1,248 and 2,229 bp in length, respectively. The amino acid sequences predicted from the open reading frames of icdI and icdII corresponded to the N-terminal amino acid sequences of the purified IDH-I and IDH-II, respectively. No homology was found between the deduced amino acid sequences of the isozymes; however, the IDH-I, a dimeric enzyme, had a high amino acid sequence identity (74.3%) to the Escherichia coli IDH. The deduced amino acid sequence of the IDH-II, a monomeric enzyme, was not related to any known sequence. However, the IDH-II had an amino acid sequence homologous to that of a cyanogen bromide-cleaved peptide containing a putative active-site methionyl residue of the monomeric IDH of Azotobacter vinelandii. The two genes (icdlI and icdII) were found to be tandemly located in the same orientation. Northern (RNA) blot analyses showed that the two genes are transcribed independently. Primer extension experiments located single transcriptional start sites 39 and 96 bp upstream of the start codons of icdI and icdII, respectively. The amount of icdI transcript but not icdII increased when Vibrio sp. strain ABE-1 cells were cultured in acetate minimal medium.

Cloning of a cDNA encoding bovine mitochondrial NADP(+)-specific isocitrate dehydrogenase and structural comparison with its isoenzymes from different species

Mitochondrial NADP(+)-specific isocitrate dehydrogenase (IDP) was co-purified with the pyruvate dehydrogenase complex from bovine kidney mitochondria. The determination of its N-terminal 16-amino-acid sequence revealed that it is highly similar to the IDP from yeast. A cDNA clone (1.8 kb long) encoding this protein was isolated from a bovine kidney lambda gt11 cDNA library using a synthetic oligodeoxynucleotide. The deduced protein sequence of this cDNA clone rendered a precursor protein of 452 amino-acid residues (50,830 Da) and a mature protein of 413 amino-acid residues (46,519 Da). It is 100% identical to the internal tryptic peptide sequences of the autologous form from pig heart and 62% similar to that from yeast. However, it shares little similarity with the mitochondrial NAD(+)-specific isoenzyme from yeast. Structural analyses of the deduced proteins of IDP isoenzymes from different species indicated that similarity exists in certain regions, which may represent the common domains for the active sites or coenzyme-binding sites. In Northern-blot analysis, one species of mRNA (about 2.2 kb for both bovine and human) was hybridized with a 32P-labelled cDNA probe. Southern-blot analysis of genomic DNAs verified simple patterns of hybridization with this cDNA. These results strongly indicate that the mitochondrial IDP may be derived from a single gene family which does not appear to be closely related to that of the NAD(+)-specific isoenzyme.

NADP-specific isocitrate dehydrogenase from the simian malaria parasite Plasmodium knowlesi: partial purification and characterization

Cell-free schizonts of Plasmodium knowlesi, a simian malaria parasite, possess significant isocitrate dehydrogenase (IDH) activity, about 90% of which is contributed by the NADP-specific enzyme that is localized in the cytosolic fraction. The enzyme has been partially purified by affinity chromatography using Blue sepharose CL-6B. Although unstable in nature, it is stabilized by citrate and glycerol. Kinetic studies with DL-isocitrate and NADP yielded hyperbolic curves with Michaelis constants of 0.210 and 0.038 mM, respectively. Manganous or magnesium ions are essential for activity. The enzyme is thermosensitive, shows maximum activity at pH 8.0, and has a molecular mass of about 48.5 kDa. It is strongly inhibited by thiol-blocking agents but protected against them by thiol-providing agents. Cupric and argentic ions also have a marked inhibitory effect on its activity. The enzyme is significantly inhibited by chloroquine and oxytetracycline in vitro, but to a lesser degree by tetracycline.

Subunit structure, expression, and function of NAD(H)-specific isocitrate dehydrogenase in Saccharomyces cerevisiae

Mitochondrial NAD(H)-specific isocitrate dehydrogenase was purified from Saccharomyces cerevisiae for analyses of subunit structure and expression. Two subunits of the enzyme with different molecular weights (39,000 and 40,000) and slightly different isoelectric points were resolved by denaturing electrophoretic techniques. Sequence analysis of the purified subunits showed that the polypeptides have different amino termini. By using an antiserum to the native enzyme prepared in rabbits, subunit-specific immunoglobulin G fractions were obtained by affinity purification, indicating that the subunits are also immunochemically distinct. The levels of NAD(H)-specific isocitrate dehydrogenase activity and immunoreactivity were found to correlate closely with those of a second tricarboxylic acid cycle enzyme, malate dehydrogenase, in yeast cells grown under a variety of conditions. S. cerevisiae mutants with defects in NAD(H)-specific isocitrate dehydrogenase were identified by screening a collection of yeast mutants with acetate-negative growth phenotypes. Immunochemical assays were used to demonstrate that one mutant strain lacks the 40,000-molecular-weight subunit (IDH1) and that a second strain lacks the 39,000-molecular-weight subunit (IDH2). Mitochondria isolated from the IDH1 and IDH2 mutants exhibited a markedly reduced capacity for utilization of either isocitrate or citrate for respiratory O2 consumption. This confirms an essential role for NAD(H)-specific isocitrate dehydrogenase in oxidative functions in the tricarboxylic acid cycle.

A highly stable NADP-dependent isocitrate dehydrogenase from Thermus thermophilus HB8: purification and general properties

NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) was purified to electrophoretic homogeneity from an extremely thermophilic bacterium, Thermus thermophilus HB8, and shown to be a dimeric protein of molecular weight 115,000, with a pI of 5.5. The amino acid composition of the present enzyme was similar to that reported for other bacterial counterparts, except for a high Arg/Lys ratio and a low Cys content. Divalent cations, such as Mn2+ and Mg2+, were essential for activity. The optimal pH was 7.8 at 55 degrees C. The Km values for NADP and D-isocitrate were 6.3 and 8.8 microM, respectively, with a Vmax of 77.6 mumol/min per mg at 55 degrees C. NAD was able to replace NADP with low efficiency. Backward reaction at 40 degrees C indicated that the Km value for 2-oxoglutarate was 63 microM with a Vmax of 4% that of the forward reaction at that temperature. The enzyme was highly stable against high temperature and denaturing reagents.

Isolation of active and inactive forms of isocitrate dehydrogenase from Escherichia coli ML 308

In Escherichia coli ML308 isocitrate dehydrogenase is partially inactivated during growth on acetate [Bennett, P.M. and Holms, W.H. (1975) J. Gen. Microbiol. 87, 37-51]. The active form of isocitrate dehydrogenase was purified to homogeneity from cells grown on glycerol. The key step in the procedure was chromatography on procion-red-Sepharose, from which the enzyme was specifically eluted with NADP+. Two forms of isocitrate dehydrogenase were purified to homogeneity from cells grown on acetate. One form did not bind to procion-red-Sepharose and was essentially inactive; this form could be resolved from the active form by non-denaturing gel electrophoresis. The other form was specifically eluted from procion-red-Sepharose and was partially active; analysis of this form by non-denaturing gel electrophoresis suggested that it was a mixture of the active and inactive forms. The three forms comigrated on denaturing gel electrophoresis and were identical by the criterion of one-dimensional peptide mapping. Analysis of the active and inactive forms by sedimentation equilibrium centrifugation and non-denaturing gel electrophoresis showed that they differed in charge but not in size. Amino acid analysis and two-dimensional peptide mapping showed that both forms were dimers of identical subunits. The active form of the enzyme contained no detectable alkali-labile phosphate, the inactive form contained 0.8 molecule/subunit and the partially active form contained an intermediate amount. The data suggest that the active and inactive forms of isocitrate dehydrogenase differ only in the presence of one phosphate group per subunit in the latter form; this is consistent with our results from phosphorylation of isocitrate dehydrogenase in vitro (Following paper in this journal). The nature of the partially active form of isocitrate dehydrogenase and the significance of the results are discussed.

NADP-specific isocitrate dehydrogenase from Escherichia coli. V. Multiple forms of the enzyme

Two forms of NADP-specific isocitrate dehydrogenase (threo-DS-isocitrate: NADP+ oxidoreductase (decarboxylating), EC 1.1.1.42) in Escherichia coli have been resolved by polyacrylamide gel isoelectric focusing and electrophoresis. Incubation of the enzyme with Mn2+ plus isocitrate prior to focusing resulted in the formation of an additional form of the enzyme, presumably the enzyme-manganese-isocitrate complex. Glycerol, a cryoprotectant used to stabilize the enzyme during purification and storage, also stabilized in during focusing, but was not necessary during electrophoresis. Thin-layer gel filtration did not reveal any differences in molecular weight between the different species of isocitrate dehydrogenase.

NADP-specific isocitrate dehydrogenase of Escherichia coli. IV. Purification by chromatography on Affi-Gel Blue

Affinity chromatography on Affi-Gel Blue has been used to purify the NADP-specific isocitrate dehydrogenase (EC 1.1.1.42) from Escherichia coli. The protocol permits rapid purification of the enzyme in milligram quantities with a yield of 50% and is carried out almost entirely at room temperature. The preparation was judged to be homogeneous by non-denaturing electrophoresis at pH 7.5 and denaturing electrophoresis in the presence of sodium dodecyl sulfate. The subunit molecular weight of 53 000, determined by sodium dodecyl sulfate gel electrophoresis, is in reasonable agreement with the value of 46 900 estimated from the amino acid composition data.

Purification and crystallization of NADP+-specific isocitrate dehydrogenase from Escherichia coli using polyethylene glycol

A simple and rapid method is presented for purifying the NADP+-dependent isocitrate dehydrogenase (threo-DS-isocitrate:NADP+ oxidoreductase (decarboxylating), from Escherichia coli, which relies on fractionation of the enzyme with polyethylene glycol. The shortened preparation results in a 32% relative recovery of purified enzyme at a specific activity of 127 micronmol/min per mg of protein. The Km values for threo-DS-isocitrate, NADP+, NAD+, Mg2+ and Mn2+ are 6.4, 36, 3000, 19.7 and 2.0 micronM, respectively. The stability of the enzyme as a function of dilution and temperature are also reported. Recrystallization of the purified enzyme under different conditions readily produces a variety of single crystals. Crystals grown from ammonium sulfate solutions belong to monoclinic space group C2 with a = 125 A, b = 111 A, c = 83.5 A and beta = 108degrees 45'. Density measurements of these crystals indicate there are two 80 000-dalton dimers per asymmetric unit.

NADP+-specific isocitrate dehydrogenase of Excherichia coli. III. Two-step purification employing affinity chromatography

The NADP+-specific isocitrate dehydrogenase (threo-DS-isocitrate:NADP+ oxidoreductase (decarboxylating), EC 1.1.1.42) of Excherichia coli has been purified to electrophoretic homogeneity by a two-step purification procedure employing affinity chromatography. The overall yield of enzyme was 30% with specific activity 125 mumol/min per ng protein. Electrophoretic homogeneity of the isocitrate dehydrogenase was deterimed in analytical polyacrylamide gels in a Tris/acetate/EDTA buffer system at pH 7.5 and in a citrate/phosphate buffer system at pH 6.0.

Properties of the nicotinamide adenine dinucleotide phosphate-specific isocitrate dehydrogenase from Blastocladiella emersonii

The nicotinamide adenine dinucleotide phosphate (NADP)-specific isocitrate dehydrogenase from Blastocladiella emersonii was purified. The enzyme was very unstable. Satisfactory stability was obtained in the presence of 0.2% ovalbumin. The enzyme had a molecular weight of about 100,000. It did not exhibit homotropic cooperativity for any of it substrates and was not affected by the allosteric modifiers citrate and adenosine monophosphate, diphosphate, and tri-phosphate. The substrate saturation studies showed both intercept and slope effects in Lineweaver-Burk plots. The Km values for isocitrate and NADP were found to be 20 and 10 muM, respectively. The product inhibition pattern was compatible with a random sequential reaction mechanism. The enzyme catalyzed the oxidative decarboxylation of isocitrate about six times better than the reductive carboxylation of alpha-ketoglutarate. The enzyme was inhibited by glyoxylate plus oxalacetate. Assays conducted in the presence of low Mg2+ concentrations exhibited a lag. This lag could be abolished by the addition of reduced NADP to the assay mixture.