Inhibition and activation of bovine heart NAD-specific isocitrate dehydrogenase by ATP

Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis

Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating the tracking of metabolic changes over time after stress in rare cells such as hematopoietic stem cells (HSCs). Here, we aimed to identify the key metabolic enzymes that define differences in glycolytic metabolism between steady-state and stress conditions in murine HSCs and elucidate their regulatory mechanisms. Through quantitative 13C metabolic flux analysis of glucose metabolism using high-sensitivity glucose tracing and mathematical modeling, we found that HSCs activate the glycolytic rate-limiting enzyme phosphofructokinase (PFK) during proliferation and oxidative phosphorylation (OXPHOS) inhibition. Real-time measurement of ATP levels in single HSCs demonstrated that proliferative stress or OXPHOS inhibition led to accelerated glycolysis via increased activity of PFKFB3, the enzyme regulating an allosteric PFK activator, within seconds to meet ATP requirements. Furthermore, varying stresses differentially activated PFKFB3 via PRMT1-dependent methylation during proliferative stress and via AMPK-dependent phosphorylation during OXPHOS inhibition. Overexpression of Pfkfb3 induced HSC proliferation and promoted differentiated cell production, whereas inhibition or loss of Pfkfb3 suppressed them. This study reveals the flexible and multilayered regulation of HSC glycolytic metabolism to sustain hematopoiesis under stress and provides techniques to better understand the physiological metabolism of rare hematopoietic cells.

Molecular insights into the catalysis and regulation of mammalian NAD-dependent isocitrate dehydrogenases

Eukaryotic NAD-dependent isocitrate dehydrogenases (NAD-IDHs) are mitochondria-localized enzymes which catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate using NAD as a cofactor. In mammals, NAD-IDHs (or IDH3) consist of three types of subunits (α, β, and γ), and exist as (α2βγ)2 heterooctamer. Mammalian NAD-IDHs are regulated allosterically and/or competitively by a diversity of metabolites including citrate, ADP, ATP, NADH, and NADPH, which are associated with cellular metabolite flux, energy demands, and redox status. Proper assembly of the component subunits is essential for the catalysis and regulation of the enzymes. Recently, crystal structures of human IDH3 have been solved in apo form and in complex with various ligands, revealing the molecular mechanisms for the assembly, catalysis, and regulation of the enzyme.

Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction

Human NAD-dependent isocitrate dehydrogenase or IDH3 (HsIDH3) catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the tricarboxylic acid cycle. It consists of three types of subunits (α, β, and γ) and exists and functions as the (αβαγ)₂ heterooctamer. HsIDH3 is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. Our previous studies have revealed the molecular basis for the activity and regulation of the αβ and αγ heterodimers. However, the molecular mechanism for the allosteric activation of the HsIDH3 holoenzyme remains elusive. In this work, we report the crystal structures of the αβ and αγ heterodimers and the (αβαγ)₂ heterooctamer containing an α-Q139A mutation in the clasp domain, which renders all the heterodimers and the heterooctamer constitutively active in the absence of activators. Our structural analysis shows that the α-Q139A mutation alters the hydrogen-bonding network at the heterodimer-heterodimer interface in a manner similar to that in the activator-bound αγ heterodimer. This alteration not only stabilizes the active sites of both α_Q139Aβ and α_Q139Aγ heterodimers in active conformations but also induces conformational changes of the pseudo-allosteric site of the α_Q139Aβ heterodimer enabling it to bind activators. In addition, the α_Q139A^ICT+Ca+NADβ^NAD structure presents the first pseudo-Michaelis complex of HsIDH3, which allows us to identify the key residues involved in the binding of cofactor, substrate, and metal ion. Our structural and biochemical data together reveal new insights into the molecular mechanisms for allosteric regulation and the catalytic reaction of HsIDH3.

Structure and allosteric regulation of human NAD-dependent isocitrate dehydrogenase

Human NAD-dependent isocitrate dehydrogenase or HsIDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. HsIDH3 exists and functions as a heterooctamer composed of the αβ and αγ heterodimers, and is regulated allosterically and/or competitively by numerous metabolites including CIT, ADP, ATP, and NADH. In this work, we report the crystal structure of HsIDH3 containing a β mutant in apo form. In the HsIDH3 structure, the αβ and αγ heterodimers form the α₂βγ heterotetramer via their clasp domains, and two α₂βγ heterotetramers form the (α₂βγ)₂ heterooctamer through insertion of the N-terminus of the γ subunit of one heterotetramer into the back cleft of the β subunit of the other heterotetramer. The functional roles of the key residues at the allosteric site, the pseudo allosteric site, the heterodimer and heterodimer-heterodimer interfaces, and the N-terminal of the γ subunit are validated by mutagenesis and kinetic studies. Our structural and biochemical data together demonstrate that the allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation of the enzyme; the activation signal from the allosteric site is transmitted to the active sites of both αβ and αγ heterodimers via the clasp domains; and the N-terminal of the γ subunit plays a critical role in the formation of the heterooctamer to ensure the optimal activity of the enzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of HsIDH3.

Molecular mechanism of the dual regulatory roles of ATP on the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase

Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) is responsible for the catalytic conversion of isocitrate into α-ketoglutarate in the Krebs cycle. This enzyme exists as the α₂βγ heterotetramer composed of the αβ and αγ heterodimers. Our previous biochemical data showed that the αγ heterodimer and the holoenzyme can be activated by low concentrations of ATP but inhibited by high concentrations of ATP; however, the molecular mechanism was unknown. Here, we report the crystal structures of the αγ heterodimer with ATP binding only to the allosteric site (α^Mgγ^Mg+CIT+ATP) and to both the allosteric site and the active site (α^Mg+ATPγ^Mg+CIT+ATP). Structural data show that ATP at low concentrations can mimic ADP to bind to the allosteric site, which stabilizes CIT binding and leads the enzyme to adopt an active conformation, revealing why the enzyme can be activated by low concentrations of ATP. On the other hand, at high concentrations ATP is competitive with NAD for binding to the catalytic site. In addition, our biochemical data show that high concentrations of ATP promote the formation of metal ion-ATP chelates. This reduces the concentration of free metal ion available for the catalytic reaction, and thus further inhibits the enzymatic activity. The combination of these two effects accounts for the inhibition of the enzyme at high concentrations of ATP. Taken together, our structural and biochemical data reveal the molecular mechanism for the dual regulatory roles of ATP on the αγ heterodimer of human NAD-IDH.

Effects of aripiprazole and clozapine on the treatment of glycolytic carbon in PC12 cells

Aripiprazole is the only atypical antipsychotic drug known to cause the phosphorylation of AMP-activated protein kinase (AMPK) in PC12 cells. However, the molecular mechanisms underlying this phosphorylation in aripiprazole-treated PC12 cells have not yet been clarified. Here, using PC12 cells, we show that these cells incubated for 24 h with aripiprazole at 50 μM and 25 mM glucose underwent a decrease in their NAD⁺/NADH ratio. Aripiprazole suppressed cytochrome c oxidase (COX) activity but enhanced the activities of pyruvate dehydrogenase (PDH), citrate synthase and Complex I. The changes in enzyme activities coincided well with those in NADH, NAD⁺, and NAD⁺/NADH ratio. However, the bioenergetic peril judged by the lowered COX activity might not be accompanied by excessive occurrence of apoptotic cell death in aripiprazole-treated cells, because the mitochondrial membrane potential was not decreased, but rather increased. On the other hand, when PC12 cells were incubated for 24 h with clozapine at 50 μM and 25 mM glucose, the NAD⁺/NADH ratio did not change. Also, the COX activity was decreased; and the PDH activity was enhanced. These results suggest that aripiprazole-treated PC12 cells responded to the bioenergetic peril more effectively than the clozapine-treated ones to return the ATP biosynthesis back toward its ordinary level. This finding might be related to the fact that aripiprazole alone causes phosphorylation of AMPK in PC12 cells.

Molecular cloning and deduced amino acid sequences of the alpha- and beta- subunits of mammalian NAD(+)-isocitrate dehydrogenase

A 153 bp fragment of the cDNA encoding the beta-subunit of pig heart NAD(+)-isocitrate dehydrogenase (NAD(+)-ICDH) was specifically amplified by PCR, using redundant oligonucleotide primers based on partial peptide sequence data [Huang and Colman (1990) Biochemistry 29, 8266-8273]. This PCR fragment was then used as a probe to isolate cDNA clones encoding the complete mature form of the beta-subunit from a monkey testis cDNA library. Examination of the deduced amino acid sequence of the monkey subunit and the partial sequence of the pig heart enzyme revealed a high level of sequence conservation. In addition, 3 overlapping fragments of the cDNA for the alpha-subunit of monkey NAD(+)-ICDH were amplified using oligonucleotide primers derived from the cDNA sequence of a subunit of bovine NAD(+)-ICDH (EMBL accession no: U07980). These cDNA fragments allow deduction of the amino acid sequence of the alpha-subunit. Since the gamma-subunit of monkey NAD(+)-ICDH has already been cloned [Nichols, Hall, Perry and Denton (1993) Biochem. J. 295, 347-350], a deduced amino acid sequence is now available for all three subunits of mammalian NAD(+)-ICDH. Interrelationships between these subunits are discussed and they are compared with the two subunits of yeast NAD(+)-ICDH and Escherichia coli NADP(+)-ICDH.

Molecular cloning and deduced amino acid sequences of the gamma-subunits of rat and monkey NAD(+)-isocitrate dehydrogenases

A 600 bp cDNA fragment encoding part of the gamma-subunit of pig heart NAD(+)-isocitrate dehydrogenase (ICDH gamma) was amplified by PCR using redundant oligonucleotide primers based on partial peptide sequence data [Huang and Colman (1990) Biochemistry 29, 8266-8273]. This PCR fragment was then used as a probe to isolate clones encoding the complete mature forms of the gamma-subunit from rat epididymis and monkey testis cDNA libraries. Comparison of the deduced amino acid sequences of the rat and monkey subunits and the partial sequence of the pig heart enzyme revealed a remarkably high level of sequence identity. The relationship between the deduced amino acid sequences of the NAD(+)-ICDH gamma-subunits and those of nonmammalian NAD(+)- and NADP(+)-ICDH subunits is discussed.

Toxicity of adenine nucleotides in the isolated perfused kidney: selective destruction of the S2 segment of the proximal tubule

In an attempt to ameliorate the morphological abnormalities and decreased renal function produced by hypoxia in the isolated perfused rat kidney, adenosine triphosphate (ATP) was added to the perfusate medium. No improvement was noted in the histological changes or renal function. Paradoxically, however, in oxygenated control kidneys, ATP (2.5-10 mM), caused a severe injury remarkably limited to the S2 segments of proximal tubule. This injury was more destructive than that observed with complete ischemia for the same period of time or with inhibitors of glycolysis, intermediary metabolism, or respiratory chain function. Tubular damage produced by ATP was paradoxically prevented by hypoxia and mitochondrial inhibition. The mechanism of this selective toxic injury to the proximal tubule remains unclear and may depend upon intact transport metabolism of the cell.

Conformations of the coenzymes and the allosteric activator, ADP, bound to NAD(+)-dependent isocitrate dehydrogenase from pig heart

NAD(+)-dependent isocitrate dehydrogenase from pig heart is an allosteric enzyme that is activated by ADP and is inhibited by NADPH in the presence of NADH. Transferred nuclear Overhauser effect measurements, made at a range of times to ensure that observed effects are due to direct dipole-dipole transfer and not to spin diffusion, were used to determine the conformations of pyridine nucleotide coenzymes and of the allosteric effector ADP. For NAD+, significant effects were observed on the N2 proton (on the nicotinamide ring) when the N1' proton (on the nicotinamide ribose) was saturated and on the N6 proton when the N2' proton was saturated, indicating that the conformation of the nicotinamide-ribose moiety is anti. The anti conformation is expected because of the stereospecificity of NAD(+)-dependent isocitrate dehydrogenase and is the same as for NADP(+)-dependent isocitrate dehydrogenase. For the adenosine moiety of NAD+, the predominant nuclear Overhauser effect on the A8 proton is found when the A2' proton is saturated. This result implies that the adenine-ribose bond is anti with respect to the ribose. Previous kinetic and binding studies of ADP activation have shown an influence of divalent metal ions. The conformation of bound ADP, in the presence of Mg2+ and/or Ca2+, is found to be anti about the adenine-ribose bond. The 3'H-8H distance increases when Ca2+ is added to the Mg-ADP-enzyme complex. Changes in the 4'H-1'H distance upon addition of isocitrate are indicative of interactions between the ADP activator site and the isocitrate site.(ABSTRACT TRUNCATED AT 250 WORDS)

Rapid purification of pig heart NAD+-isocitrate dehydrogenase. Studies on the regulation of activity by Ca2+, adenine nucleotides, Mg2+ and other metal ions

1. A new procedure for purifying pig heart NAD+-isocitrate dehydrogenase from mitochondrial extracts has been developed. This relies on the use of f.p.l.c. techniques and exploits the hydrophobic properties of the gel-filtration medium Superose 6 at high ionic strength. A 300-fold purification to apparent homogeneity is achieved within 5 h and with a yield of greater than 20%. 2. The enzyme had an apparent native molecular mass on gel filtration of 320 kDa. In agreement with previous studies [Ramachandran & Colman (1980) J. Biol. Chem. 255, 8859-8864], three subunits (all close to 38 kDa) were separable by isoelectric focusing 3. This preparation was used to investigate the effects of adenine nucleotides, KCl and the required bivalent metal ions, Mg2+ and Mn2+, on the regulation of the enzyme by Ca2+. 4. In the presence of 1.5 mM-ADP, increasing the concentration of Mg2+ from 20 microM to 6.0 mM raised the concentration of Ca2+ required for half-maximal effect (K0.5 value) from 1.2 microM to 232 microM. Similarly, in the presence of 2.5 microM-Mn2+, a K0.5 value for Ca2+ of 3.3 microM was obtained, and this value was increased to 8.9 microM in the presence of 100 microM-Mn2+. In the presence of 1 mM-Mg2+ and 1.5 mM-ADP, the K0.5 value for Ca2+ was raised from 4.7 microM to 10 microM by 75 mM-KCl.

Regulation of NAD+-linked isocitrate dehydrogenase and 2-oxoglutarate dehydrogenase by Ca2+ ions within toluene-permeabilized rat heart mitochondria. Interactions with regulation by adenine nucleotides and NADH/NAD+ ratios

1. Toluene-permeabilized rat heart mitochondria have been used to study the regulation of NAD+-linked isocitrate dehydrogenase and 2-oxoglutarate dehydrogenase by Ca2+, adenine and nicotinamide nucleotides, and to compare the properties of the enzymes in situ, with those in mitochondrial extracts. 2. Although K0.5 values (concn. giving half-maximal effect) for Ca2+ of 2-oxoglutarate dehydrogenase were around 1 microM under all conditions, corresponding values for NAD+-linked isocitrate dehydrogenase were in the range 5-43 microM. 3. For both enzymes, K0.5 values for Ca2+ observed in the presence of ATP were 3-10-fold higher than those in the presence of ADP, with values increasing over the ADP/ATP range 0.0-1.0. 4. 2-Oxoglutarate dehydrogenase was less sensitive to inhibition by NADH when assayed in permeabilized mitochondria than in mitochondrial extracts. Similarly, the Km of NAD+-linked isocitrate dehydrogenase for threo-Ds-isocitrate was lower in permeabilized mitochondria than in extracts under all the conditions investigated. 5. It is concluded that in the intact heart Ca2+ activation of NAD+-linked isocitrate dehydrogenase may not necessarily occur in parallel with that of the other mitochondrial Ca2+-sensitive enzymes, 2-oxoglutarate dehydrogenase and the pyruvate dehydrogenase system.

NAD(+)-linked isocitrate dehydrogenase in fish tissues

NAD(+)-linked isocitrate dehydrogenase was found in the brain, heart, gills, kidney, liver and muscle of trout, and in the liver and muscle of eel. A complex homogenization buffer containing 1 mM ADP, 5 mM MgSO4, 5 mM citrate and 40% glycerol is required for retrieval of significant amounts of stable enzyme. The highest activities were found in brain of trout and the lowest in white muscle of trout and eel. The enzyme was partially purified from frozen trout heart to a final activity of 0.04 μM/min/mg protein, and the kinetic properties of this partially purified enzyme were studied. The enzyme requires either Mn(2+) or Mg(2+) for activity, higher activities being observed with Mn(2+). Saturation kinetics for DL-isocitrate were sigmoidal, apparent S0·5=8.2±0.6 mM and nH=1.8±0.2, in the absence of ADP, changing to hyperbolic, apparent S0·5=1.4±0.3 mM and nH=1.0, with 1 mM ADP added. Citrate and Ca(2+) were found to activate the enzyme to a small extent. NADH strongly inhibited the enzyme, I50=3.7±0.5 μM. ATP was also found to be an inhibitor, I50=7.2±1.4 mM. These properties are consistent with the role of the enzyme as a major control site of the tricarboxylic acid cycle.

Activity of purified NAD-specific isocitrate dehydrogenase at modulator and substrate concentrations approximating conditions in mitochondria

The kinetic parameters of NAD-specific isocitrate dehydrogenase from bovine heart were examined at levels of substrates and effectors approximating the concentrations reported for isolated intact heart mitochondria in different respiratory states. The effect of changing ADP/ATP ratios (with total adenine nucleotides constant at 8 mmol/L) on enzyme activity was measured at constant concentrations of the substrates magnesium D-isocitrate (0.10 mmol/L) and NAD+ (3.0 mmol/L), the positive effector magnesium citrate (1.0 mmol/L) and the negative effector NADPH (1.5 mmol/L) at pH 7.4. Enzyme activity increased with increasing ADP/ATP ratios as a result of activation by rising ADP concentrations and not due to decreasing inhibition by falling levels of ATP. Increasing ADP decreased the inhibition by NADPH, and this effect was enhanced by magnesium citrate and by free Ca2+. In incubation media containing all of the above effectors, the S0.5 for enhancement of activity by free Ca2+ was 10 to 20 mumol/L at ratios of total ADP/total ATP between 2.0 and 0.1. This value is in the range of intramitochondrial concentrations of free Ca2+,1 but it is appreciably larger than S0.5 of Ca2+ (0.6 to 1 mumol/L) for the enhancement of ADP activation, which was determined in the absence of other effectors. When both the NAD+/NADH and the ADP/ATP ratios were decreased, a further decline in activity was found. The effect of the decreasing NAD+/NADH ratio was due to inhibition by NADH (apparent I0.5 = 0.23 +/- 0.03 mmol/L) since NAD+ was saturating over the range examined.