The role of isozymes in metabolism: a model of metabolic pathways as the basis for the biological role of isozymes

A kinetic rationale for functional redundancy in fatty acid biosynthesis

Cells build fatty acids with biocatalytic assembly lines in which a subset of enzymes often exhibit overlapping activities (e.g., two enzymes catalyze one or more identical reactions). Although the discrete enzymes that make up fatty acid pathways are well characterized, the importance of catalytic overlap between them is poorly understood. We developed a detailed kinetic model of the fatty acid synthase (FAS) of Escherichia coli and paired that model with a fully reconstituted in vitro system to examine the capabilities afforded by functional redundancy in fatty acid synthesis. The model captures-and helps explain-the effects of experimental perturbations to FAS systems and provides a powerful tool for guiding experimental investigations of fatty acid assembly. Compositional analyses carried out in silico and in vitro indicate that FASs with multiple partially redundant enzymes enable tighter (i.e., more independent and/or broader range) control of distinct biochemical objectives-the total production, unsaturated fraction, and average length of fatty acids-than FASs with only a single multifunctional version of each enzyme (i.e., one enzyme with the catalytic capabilities of two partially redundant enzymes). Maximal production of unsaturated fatty acids, for example, requires a second dehydratase that is not essential for their synthesis. This work provides a kinetic, control-theoretic rationale for the inclusion of partially redundant enzymes in fatty acid pathways and supplies a valuable framework for carrying out detailed studies of FAS kinetics.

Metabolic isoenzyme shifts in cancer as potential novel therapeutic targets

The functional redundancy of metabolic enzyme expression may present a new strategy for developing targeted therapies in cancer. To satisfy the increased metabolic demand required during neoplastic transformations and proliferation, cancer cells may rely on additional isoforms of a metabolic enzyme to satisfy the increased demand for metabolic precursors, which could subsequently render cancer cells more vulnerable to isoform-specific inhibitors. In this review, we provide a survey of common isoenzyme shifts that have been reported to be important in cancer metabolism and link those to metabolic pathways that currently have drugs in various stages of development. This phenomenon suggests a potentially new therapeutic strategy for the treatment of cancer by identifying shifts in the expression of metabolic isoenzymes between cancer and normal cells. We also delineate other putative metabolic isoenzymes that could be targets for novel targeted therapies for cancer. Changes in isoenzyme expression that occur during neoplastic transformations or in response to environmental pressure in cancer cells may result in isoenzyme diversity that may subsequently render cancer cells more vulnerable to isoform-specific inhibitors due to reliance on a single isoform to perform a vital enzymatic function.

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

The aspartate-derived amino-acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non-intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration.

Spermatogenic cell-specific type 1 hexokinase is the predominant hexokinase in sperm

Hexokinase is the first enzyme in the glycolytic pathway and utilizes ATP to convert glucose to glucose-6-phosphate (G6P). We previously identified three variant transcripts of Hk1 that are expressed specifically in spermatogenic cells, have different 5' untranslated regions, and encode a protein (HK1S, spermatogenic cell-specific type 1 hexokinase) in which the porin-binding domain (PBD) of HK1 is replaced by a novel N-terminal spermatogenic cell-specific region (SSR). However, the level of expression of the individual variant transcripts or of the other members of the hexokinase gene family (Hk2, Hk3, and Gck) in spermatogenic cells remains uncertain. We show that Hk1, Hk2, and Hk3 transcripts levels are quite low in spermatocytes and spermatids and Gck transcripts are relatively abundant in spermatids, but that glucokinase (GCK) is not detected in spermatozoa. Using real time RT-PCR (qPCR) with primers specific for each of the three variant forms and RNA from whole testis and isolated germ cells, we found that transcripts for Hk1_v2 and Hk1_v3, but not for Hk1_v1, are relatively high in spermatids. Similar results were seen using spermatogenic cells isolated by laser-capture microdissection (LCM). Immunoblotting studies found that HK1S is abundant in sperm, and immunostaining confirmed that HK1S is located mainly in the principal piece of the sperm flagellum, where other spermatogenic cell-specific glycolytic enzymes have been found. These results strongly suggest that HK1, HK2, HK3, and GCK are unlikely to have a role in glycolysis in sperm and that HK1S encoded by Hk1_v2 and Hk1_v3 serves this role.

Isozymes of mammalian hexokinase: structure, subcellular localization and metabolic function

The first step in metabolism of glucose (Glc) is usually phosphorylation, catalyzed by hexokinase. However, the Glc-6-P produced can then enter one or more of several alternative pathways. Selective expression of isozymic forms of hexokinase, differing in catalytic and regulatory properties as well as subcellular localization, is likely to be an important factor in determining the pattern of Glc metabolism in mammalian tissues/cells. Despite their overall structural similarity, the Type I, Type II and Type III isozymes differ in important respects. All three isozymes are inhibited by the product, Glc-6-P, but with the Type I isozyme, this inhibition is antagonized by P(I), whereas with the Type II and Type III isozymes, P(i) actually causes additional inhibition. Reciprocal changes in intracellular levels of Glc-6-P and P(i) are closely associated with cellular energy status, and it is proposed that the response of the Type I isozyme to these effectors adapts it for catabolic function, introducing Glc into glycolytic metabolism for energy production. In contrast, the Type II, and probably the Type III, isozymes are suggested to serve primarily anabolic functions, e.g. to provide Glc-6-P for glycogen synthesis or metabolism via the pentose phosphate pathway for lipid synthesis. Type I hexokinase binds to mitochondria through interaction with porin, the protein that forms channels through which metabolites traverse the outer mitochondrial membrane. Several experimental approaches have led to the conclusion that the Type I isozyme, bound to actively phosphorylating mitochondria, selectively uses intramitochondrial ATP as substrate. Such interactions are thought to facilitate coordination of the introduction of Glc into glycolysis, via the hexokinase reaction, with the terminal oxidative stages of Glc metabolism occurring in the mitochondria, thus ensuring an overall rate of Glc metabolism commensurate with cellular energy demands and avoiding excessive production of lactate. The Type II isozyme also binds to mitochondria. Whether such coupling occurs with mitochondrially bound Type II hexokinase in normal tissues, and how it might be related to the proposed anabolic role of this isozyme, remain to be determined. The Type III isozyme lacks the hydrophobic N-terminal sequence known to be critical for binding of the Type I and Type II isozymes to mitochondria. Immunolocalization studies have indicated that, in many cell types, the Type III has a perinuclear localization, the possible metabolic consequences of which remain unclear.

Localization of the fructose 1,6-bisphosphatase at the nuclear periphery

The localization of fructose 1,6-bisphosphatase (D-Fru-1,6-)2-1-phosphohydrolase, EC 3.1.3.11) in rat kidney and liver was determined immunohistochemically using a polyclonal antibody raised against the enzyme purified from pig kidney. The immunohistochemical analysis revealed that the bisphosphatase was preferentially localized in hepatocytes of the periportal region of the liver and was absent from the perivenous region. Fructose-1,6-bisphosphatase was also preferentially localized in the cortex of the kidney proximal tubules and was absent in the glomeruli, loops of Henle, collecting and distal tubules, and in the renal medulla. As indicated by immunocytochemistry using light microscopy and confirmed with the use of reflection confocal microscopy, the enzyme was preferentially localized in a perinuclear position in the liver and the renal cells. Subcellular fractionation studies followed by enzyme activity assays revealed that a majority of the cellular fructose-1,6-bisphosphatase activity was associated to subcellular particulate structures. Overall, the data support the concept of metabolic zonation in liver as well as in kidney, and establish the concept that the Fructose-1,6-bisphosphatase is a particulate enzyme that can not be considered a soluble enzyme in the classical sense.

Isotopic methods for probing organization of cellular metabolism

These examples serve to illustrate that it is now possible to investigate metabolism in intact tissues using a variety of biophysical methods. While we have concentrated on NMR methods, reflecting our own interests in using 13C as a metabolic tracer, GC-mass spectroscopy can often provide similar metabolic information and has the advantage of increased sensitivity over NMR. Combining either or both of these technologies with cleaver 'chemical biopsy' methods offers new opportunities to examine what may seem to be old metabolic questions in a much more relevant environment, the native state.

Metabolic consequences of enzyme interactions

The fact that enzyme complexes, stable, quasi-stable, and dynamic, exist in cells can no longer be ignored. Experimental evidence done with a variety of techniques has demonstrated these interactions in vitro and in vivo. There is scarcely a single known metabolic pathway in which no interactions of any of its enzymes exist (see reference 27 for a list of these). Such interactions are not only ubiquitous throughout metabolism, but they exist in all cell types, procaryote and eucaryote. In many of these systems the advantages of and regulatory power of enzyme-enzyme or enzyme-structural protein interactions has been amply demonstrated. The more difficult task is to assess accurately quantitative aspects of a system that varies between the solid, gel, and aqueous state. It is clear that the metabolic paradigm of soluble randomly dispersed metabolic elements in cells must be replaced, and new theoretical and experimental approaches introduced into this vital area of biological research.

Identification of a multienzyme complex of the tricarboxylic acid cycle enzymes containing citrate synthase isoenzymes from Pseudomonas aeruginosa

A multienzyme complex of tricarboxylic acid cycle enzymes, catalysing the consecutive reactions from fumarate to 2-oxoglutarate, has been identified in extracts of Pseudomonas aeruginosa prepared by gentle osmotic lysis of the cells. The individual enzyme activities of fumarase, malate dehydrogenase, citrate synthase, aconitase and isocitrate dehydrogenase can be used to reconstitute the complex. The citrate synthase isoenzymes, CSI and CSII, from this organism can be used either together or as the individual activities to reconstitute the complex. No complex can be reformed in the absence of CSI or CSII. Which CS isoenzyme predominates in the complex depends on the phase of growth at which the cells were harvested and the extract prepared. More CSI was found in the complex during exponential growth, whereas CSII predominated during the stationary phase. The results support the idea of a 'metabolon' in this organism, with the composition of the CS component varying during the growth cycle.

Mapping of isozymic differences in enolase

The existence of the isozymes of non-regulatory enzymes often has been linked to their interaction with other macromolecules. Enolase, a non-regulatory enzyme, has three isozymes for which sequences have been determined in two or more vertebrate species. The positions in the enolase sequences that differ between the isozymes were mapped in the 3-D structure of the enzyme. The positions in a given isozymic form which were not conserved in different species were considered to be resulting from the neutral drift of sequences and rejected. Also, the residues with no accessible surface were rejected. Three areas with relatively high densities of isozymic substitutions were found. We consider them as the likely sites of contact with other macromolecules.

Modulation of lactate dehydrogenase activity by enzyme-protein interaction

Some lactate dehydrogenase modulator proteins have been isolated from the lactate dehydrogenase-free crude mitochondrial fraction of rabbit muscle, beef liver and chicken liver. It was shown that beef and chicken liver mitochondrial extracts exhibited activatory capacity in contrast to the inhibitory capacity of rabbit muscle mitochondrial extracts. All modulators can be precipitated by 80% ammonium sulphate saturation and show high anodic electrophoretic mobility and heat stability. Modulators have higher affinity for alkaline pI lactate dehydrogenase isoenzymes, independent of whether the M and H subunits are predominant. The inhibitor and the activator molecules compete for lactate dehydrogenase since their modulatory capacity was nullified when similar relative amounts were used. This study shows the existence of analogous proteins with an acidic pI in the different mitochondrial fractions which modify lactate dehydrogenase activity.

Hexokinase isoenzymes from the Novikoff hepatoma. Purification, kinetic and structural characterization, with emphasis on hexokinase C

The purification to homogeneity of hexokinases B and C from the cytosol of rat Novikoff hepatoma was achieved by a protocol using an initial chromatography on Blue 2-agarose to separate the isoenzymes from each other. After that step each hexokinase was subjected to chromatography on DEAE-cellulose, hydroxyapatite and Sephacryl S-300, followed by re-chromatography on hydroxyapatite. The final preparations of hexokinases B and C had specific activities of 86 and 23.5 units/mg of protein respectively, and gave single bands on electrophoresis under non-denaturing conditions or in SDS/polyacrylamide gels. Mr values of about 100,000 were found for both isoenzymes either by Sephacryl S-300 chromatography or by SDS/polyacrylamide-gel electrophoresis. Values of apparent Km for glucose and ATP of pure hexokinase B were similar to those reported for the enzyme from other sources. The apparent Km value for glucose of hexokinase C was 0.025 mM. Marked inhibition of hexokinase C by glucose concentrations above 0.2 mM was found. The effect was partially relieved by ATP concentrations above 1 mM and was independent of pH. Glucose 6-phosphate was inhibitory, but the Ki value (0.18 mM) is higher than those reported for other animal hexokinases. The amino acid composition of hexokinase C was found to be similar to those reported for hexokinases B and D. Also, an immune serum directed against hexokinase A was able, at low dilutions, to bind hexokinases B and C. An immune serum directed against hexokinase C was able, at low dilutions, to bind hexokinase B and also, but weakly, hexokinase A.

Interaction of immobilized phosphofructokinase with soluble muscle proteins

Selected glycolytic enzymes (including phosphoglucose isomerase, aldolase, glyceraldehyde phosphate dehydrogenase, enolase, pyruvate kinase and lactate dehydrogenase), as well as glycogen phosphorylase, creatine kinase, and adenylate kinase, bound to phosphofructokinase immobilized on an agarose gel. The affinity of phosphofructokinase to these various proteins differed, with phosphorylase exhibiting the strongest binding. Binding was reversed either by: (1) elution with high-ionic-strength buffer (0.4 M KCl); (2) the addition of a 5-10 mM concentration of ATP; or (3) high concentrations of fructose 6-phosphate (5 mM).

A comparison of the evolutionary distribution of the two neuroendocrine markers, neurone-specific enolase and protein gene product 9.5

One- and two-dimensional polyacrylamide gel electrophoresis followed by immunoblotting has been used to examine the phylogenetic distribution of the two neuronal and neuroendocrine proteins, neurone-specific enolase and protein gene product 9.5, in animal brains. A new immunoblotting procedure was used in which complex two-dimensional patterns of brain proteins were transferred to nitrocellulose paper simultaneously with the Coomassie Blue stain. This produced a copy of the blue spot pattern against which brown protein spots reacting in a specific antibody-immunoperoxidase procedure could be identified unequivocally. Extracts of human, bovine, sheep, rabbit, rat, guinea-pig, chicken, trout, and frog brains were examined. Proteins cross-reacting with antisera to the human forms of both proteins could be demonstrated in all species examined. This suggests that proteins corresponding to neurone-specific enolase and protein gene product 9.5 could have evolved at least 400 million years ago and have been highly conserved throughout evolution.

Stability of hexokinases A, B and C and N-acetylglucosamine kinase in liver cells isolated from rats submitted to diabetes and several dietary conditions

The effect of dietary and hormonal variations on the specific activities of hexokinase isoenzymes, N-acetylglucosamine kinase and pyruvate kinase isoenzymes in parenchymal and non-parenchymal liver cells was studied. Hexokinase D was markedly decreased in hepatocytes from animals fasted or fed on the carbohydrate-free diet as well as from diabetic rats, attaining a constant low level of about 17% of normal values. Pyruvate kinase L was also diminished in hepatocytes under the same experimental conditions. In contrast, the three high-affinity hexokinase isoenzymes A, B and C remained without variation in total amount or in their relative proportions in hepatocytes and non-parenchymal liver cells isolated from animals under the various conditions studied. N-Acetylglucosamine kinase activities also did not change either in parenchymal or in non-parenchymal liver cells under all conditions. The results are discussed in relation to the significance of N-acetylglucosamine kinase and the various hexokinase isoenzymes for the phosphorylation of glucose after dietary and hormonal manipulations.

Interactions between glycolytic enzymes and components of the cytomatrix

Evidence is provided that enzymes absorb to cellular structures in a wide range of tissues. In particular, the interactions between glycolytic enzymes and the microfilaments of the cytoplasm are described. The relevance of these interactions to the compartmentation of carbohydrate metabolism is discussed. Examples are given of the variations in degree of binding during alteration of tissue metabolism and, for individual glycolytic enzymes, during fetal development and differentiation. Overall, these data support the concept that metabolic activities in the cytoplasm have an organized structure. Just as the structural elements of the cytosolic compartment have evolved with the capacity to assemble and disassemble in response to the changing requirements of the organism, so the metabolic elements appear to have evolved a parallel system that provides for the appropriate positioning of an energy-producing sequence in relation to the specific, dynamic requirements of the cytoskeleton.

The physiological role of the isoenzymes of lactate dehydrogenase in potatoes

Four of the five isoenzymes of lactate dehydrogenase present in potato tubers have been isolated and their kinetic properties examined. The pyruvate-reductase activity of isoenzyme-4 is greatly reduced at low pH, the affinity for both pyruvate and NADH is reduced and ATP has a stronger inhibitory effect. If the design properties of an enzyme dictate a high affinity for substrates, then the Km values for lactate, glyoxylate and NAD are consistent with an oxidative role for isoenzyme-4. The same considerations do not permit a conclusion about the physiological role of isoenzymes-1 to-3. However, an overview of the kinetic properties of these isoenzymes indicates that isoenzyme-1 is best adapted for the role of pyruvate reductase. Consideration of the relationships between kinetic constants and electrophoretic mobilities of the isoenzymes, leads us to predict that isoenzyme-5 is well adapted for a role in the oxidation of lactate or glyoxylate. The lactate dehydrogenase of potato leaves appears to consist prodominantly of an isoenzyme with the same mobility as isoenzyme-2 of the tubers and the two isoenzymes are probably identical. The kinetic properties of this isoenzyme are consistent with roles in either oxidation or reduction.

Saccharomyces carlsbergensis fdp mutant and futile cycling of fructose 6-phosphate

In Saccharomyces, the addition of glucose to cells grown in media lacking sugars causes irreversible inactivation of fructose bisphosphatase. One function of this process might be to prevent a futile cycle of formation and hydrolysis of fructose 1,6-bisphosphate. We tested such cycling by assessing the labeling of the 1-position of glucose in polysaccharides from [6-14C]glucose (J.P. Chambost and D. G. Fraenkel, J. Biol. Chem. 225:2867-2869, 1980) by using mutants impaired in glucose growth and known not to inactivate the phosphatase normally (i.e., the fdp mutant of Saccharomyces carlsbergensis [van de Poll et al., J. Bacteriol. 117:965-970, 1974] and the similar cif mutant of Saccharomyces cerevisiae [Navon et al., Biochemistry 18:4487-4499, 1979] ), as well as in the wild-type strain tested in the 1-h period before inactivation is complete. There was marginal, if any, cycling in any situation, and we conclude that the phosphatase activity is controlled by means other than inactivation or that the extent of cycling is too low to be significant, or both. For the fdp mutant data are also presented on growth, rate of glucose metabolism, metabolite accumulations, enzyme levels, and glucose transport, but the primary lesion is unknown.

Saccharomyces carlsbergensis fdp mutant and futile cycling of fructose 6-phosphate

In Saccharomyces, the addition of glucose to cells grown in media lacking sugars causes irreversible inactivation of fructose bisphosphatase. One function of this process might be to prevent a futile cycle of formation and hydrolysis of fructose 1,6-bisphosphate. We tested such cycling by assessing the labeling of the 1-position of glucose in polysaccharides from [6-14C]glucose (J.P. Chambost and D. G. Fraenkel, J. Biol. Chem. 225:2867-2869, 1980) by using mutants impaired in glucose growth and known not to inactivate the phosphatase normally (i.e., the fdp mutant of Saccharomyces carlsbergensis [van de Poll et al., J. Bacteriol. 117:965-970, 1974] and the similar cif mutant of Saccharomyces cerevisiae [Navon et al., Biochemistry 18:4487-4499, 1979] ), as well as in the wild-type strain tested in the 1-h period before inactivation is complete. There was marginal, if any, cycling in any situation, and we conclude that the phosphatase activity is controlled by means other than inactivation or that the extent of cycling is too low to be significant, or both. For the fdp mutant data are also presented on growth, rate of glucose metabolism, metabolite accumulations, enzyme levels, and glucose transport, but the primary lesion is unknown.

The comparative isozymology of vertebrate hexokinases

1. Multiple hexokinase isozymes have been found in most vertebrates. Since each isozyme displays distinctive structural, kinetic and regulatory characteristics, the system qualifies as a useful probe for studies on molecular evolution. 2. At least seven types of chromatographic patterns of liver hexokinases have been observed in mammals. In contrast, each Class of lower vertebrates present only two or three distinct profiles. 3. Aves and higher Reptiles do not have the same hexokinase isozymes as other vertebrates. The nature of the differences is poorly understood. 4. Ontogenetic changes of liver hexokinase profiles are quite different in rat, chick and frog. 5. Structural comparisons of three vertebrate hexokinases having a molecular weight of approximately 100,000 suggest that those isozymes originated from a pre-vertebrate ancestor through gene duplication followed by fusion and further duplication events. Another hexokinase (the so-called glucokinase), with half the molecular weight, may have arisen either as the result of subsequent even splitting of the fused gene or, less probably, by divergence from a duplicated gene before the fusion event.

Biosynthesis of pyruvate kinase isozymes in rat liver

1. The L and M1 isozymes of pyruvate kinase were purified to homogeneity from rat liver and muscle respectively and their specific antibodies were employed to quantify the isozyme concentration in rat liver during development. 2. Total enzyme activity decreases towards birth and reaches a minimum on the 3rd postnatal day, but the activity increases dramatically after weaning. 3. Immunoprecipitation revealed that the M2 type predominates in the prenatal period but decreases sharply just before birth. 4. The L isozyme contribution is augmented upon weaning and is sustained until the rat is adult and a L/M ratio of 9:1 is maintained. 5. By means of incorporation studies with [3H]leucine followed by immunoprecipitation, the increase in L-type activity when approaching term and after weaning is explained by a twofold increase in its rate of synthesis coupled with a concomitant reduction of the M2-type synthesis.

Kinetic aspects of soluble dehydrogenases requiring nicotinamide coenzymes

Methods for establishing the kinetic mechanisms of dehydrogenase reactions are dealt with in general terms. Examples ranging from relatively simple to obviously complex enzymes, and showing various mechanistic features of interest and importance are discussed.