Malic enzyme from the rat tapeworm, Hymenolepis diminuta, has been purified 320-fold to a final specific activity of 29.4. The purification procedure included heat treatment, followed by column chromatography with Sephadex G-20, two phosphocellulose columns, and Sephadex G-200, respectively. The final purified enzyme appeared to be homogeneous on disc gel electrophoresis and G-200 gel filtration.

The NAD+-linked malic enzyme from Ascaris suum has been studied with regard to its kinetic and catalytic properties. Possible relationships between these properties and the physiological functioning of the malic enzyme were examined.

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The kinetic mechanism of activation of the NAD-malic enzyme by fumarate and the transition state structure for the oxidation malate for the NAD-malic enzyme reaction have been studied. Fumarate exerts its activating effect by decreasing the off-rate for malate from the E:Mg:malate and E:Mg:NAD:malate complexes. The activation by fumarate results in a decrease in K_imalate and an increase in V/K_malate by about 2-fold, while the maximum velocity remains constant. A discrimination exists between active and activator sites for the binding of dicarboxylic acids. Activation by fumarate is proposed to have physiologic importance in the parasite. The hydride transfer transition state for the NAD-malic enzyme reaction is concerted with respect to solvent isotope sensitive and hydride transfer steps. Two protons are involved in the solvent isotope sensitive step, one with a normal fractionation factor, another with an inverse fractionation factor. A structure for the transition state for hydride transfer in the NAD-malic enzyme reaction is proposed.

Transvection, a chromosome pairing-dependent form of trans-based gene regulation, is widespread in the Drosophila melanogaster genome. Recent studies demonstrate that transvection is sensitive to cell environment and type in D. melanogaster, implicating transvection as a complex trait. To test this possibility, we first established that trans-interactions previously documented at the Malic enzyme (Men) locus are transvection (i.e., pairing-dependent). We then characterized the sensitivity of transvection at the Men locus to changes in the environment (temperature) and genetic background (third chromosome). Transvection varied significantly across genetic backgrounds and was significantly reduced by changes in temperature, and the two factors interacted to further modify transvection, while cis-based gene regulation remained unchanged by temperature. To determine if differences in transvection observed across genetic background and temperature are related to their effects on transcription factor expression, and possibly the presence or absence of binding sites for these transcription factors within the Men locus, we tested the relationship between Men expression and five transcription factors with binding sites near the Men transcription start sit (TSS). We found correlations between the expression of at least one transcription factor, Abd-B, and the presence of binding sites for that factor, and Men expression across changes in the environment. We also determined that changes in Abd-B expression can directly affect Men expression in cis, suggesting that cis and trans-regulation can share regulatory components in at least some cases. Together, our findings stress the importance of studying genetic interactions from a dynamic perspective by incorporating both genetic and environmental variation.

Drought is a major environmental factor limiting crop productivity. Considering a significant area of crop production under water-limited rained conditions, there is a great need to develop production systems to sustain yield potentials under drought stress. Silicon has recently been recognized as an important element in plant nutrition. In this study, it was shown that supplying soybean with soluble silicon in the soil could improve vegetative growth and drought tolerance under water limiting conditions. In order to understand the molecular mechanism how silicon alleviates drought stress, the effects of silicon application on protein expression and antioxidant enzymes were examined. Soybean plants were grown in sand-containing pots supplied with 4 millimolar solutions of sodium silicate. To cancel the effect of sodium, the same amount of sodium chloride was used along with control plants. Soluble proteins were isolated from the leaves and roots of silicon-treated and control plants subjected to water deficit stress. Two-dimensional gel electrophoresis and mass spectrometry approaches were used to identify differentially expressed leaf and root proteins in response to silicon application under water deficit stress. Proteins that showed differential expression in response to silicon application included metabolic enzymes and proteins involved in the proteasome-dependent degradation pathway. These results indicate that silicon application could affect enzymes important for carbohydrate metabolism and stabilize aldehyde dehydrogenases and malic enzyme under water deficit stress, which may be attributable to drought tolerance.

Stopped-flow experiments in which the NAD-malic enzyme was preincubated with different reactants at near saturating substrate concentrations suggest a slow isomerization of the E:NAD:Mg complex. The lag is eliminated by preincubation with Mg˙² and malate suggesting that the formation of E:Mg:Malate either bypasses or speeds up the slow isomerization step. Circular dichroic spectral studies of the secondary structural changes of the native enzyme in the presence and absence of substrates supports the existence of conformational changes with NAD˙ and malate. Thus, a slow conformational change of the E:NAD:Mg complex is likely one of the rate-limiting steps in the pre-steady state.

The isotope partitioning studies of the Ascaris suum NAD-malic enzyme reaction were examined with five transitory complexes including E:NAD, E:NAD:Mg, E:malate, E:Mg:malate, and E:NAD:malate. Three productive complexes, E:NAD, E:NAD:Mg, and E:Mg:malate, were obtained, suggesting a steady-state random mechanism. Data for trapping with E:14C-NAD indicate a rapid equilibrium addition of Mg2+ prior to the addition of malate. Trapping with 14C-malate could only be obtained from the E:Mg2+:14C-malate complex, while no trapping from E:14C-malate was obtained under feasible experimental conditions. Most likely, E:malate is non-productive, as has been suggested from the kinetic analysis. The experiment with E:NAD:malate could not be carried out due to the turnover of trace amounts of malate dehydrogenase in the pulse solution. The equations for the isotope partitioning studies varying two substrates in the chase solution in an ordered terreactant reaction were derived, allowing a determination of the relative rates of substrate dissociation to the catalytic reaction for each of the productive transitory complexes. NAD and malate are released from the central complex at an identical rate, equal to the catalytic rate.

Dissociation constants for alternate dirmcleotide substrates and competitive inhibitors suggest that the dinucleotide binding site of the Ascaris suum NAD-malic enzyme is hydrophobic in the vicinity of the nicotinamide ring. Changes in the divalent metal ion activator from Mg^2+ to Mn^2+ or Cd^2+ results in a decrease in the dinucleotide affinity and an increase in the affinity for malate. Primary deuterium and 13-C isotope effects obtained with the different metal ions suggest either a change in the transition state structure for the hydride transfer or decarboxylation steps or both. Deuterium isotope effects are finite whether reactants are maintained at saturating or limiting concentrations with all the metal ions and dinucleotide substrates used. With Cd^2+ as the divalent metal ion, inactivation of the enzyme occurs whether enzyme alone is present or is turning over. Upon inactivation only Cd^2+ ions are bound to the enzyme which becomes denatured. Modification of the enzyme to give an SCN-enzyme decreases the ability of Cd^2+ to cause inactivation. The modified enzyme generally exhibits increases in K_NAD and K_i_metai and decreases in V_max as the metal size increases from Mg^2+ to Mn^2+ or Cd^2+, indicative of crowding in the site. In all cases, affinity for malate greatly decreases, suggesting that malate does not bind optimally to the modified enzyme. For the native enzyme, primary deuterium isotope effects increase with a concomitant decrease in the 13-C effects when NAD is replaced by an alternate dinucleotide substrate different in redox potential. This suggests that when the alternate dinucleotides are used, a switch in the rate limitation of the chemical steps occurs with hydride transfer more rate limiting than decarboxylation. Deuteration of malate decreases the 13-C effect with NAD for the native enzyme, but an increase in 13-C effect is obtained with alternate dinucleotides. These suggest the presence of a secondary 13-C effect in the hydride transfer step. This phenomenon is also applicable to the modified enzyme with NAD as the substrate.

<p>Apoptosis is a conserved mode of cell death executed by a group of proteases named caspases, which collectively ensure tissue homeostasis in multicellular organisms by triggering a program of cellular "suicide" in response to developmental cues or cellular damage. </p><p>Accumulating evidence suggests that cellular metabolism impinges directly upon the decision to initiate cell death. Several links between apoptosis and metabolism have been biochemically characterized. Using <italic>Xenopus</italic> oocyte extracts, our laboratory previously discovered that caspase-2 is suppressed by NADPH metabolism through an inhibitory phosphorylation at S164. However, the physiological relevance of these findings has not been investigated at the whole organism level. Studies presented in this dissertation utilize both Schneider's <italic>Drosophila</italic> S2 (S2) cells and transgenic animals to untangle the influence of metabolic status on fly apoptosis.</p><p>We first demonstrate a novel link between <italic>Drosophila</italic> apoptosis and metabolism by showing that cellular NADPH levels modulate the fly initiator caspase Dronc through its phosphorylation at S130. Biochemically and genetically blocking NADPH production removed this inhibitory phosphorylation, resulting in the activation of Dronc and the subsequent apoptotic cascade in cultured S2 cells and specific neuronal cells in transgenic animals. Similarly, non-phosphorylatable Dronc was found to be more potent than wild-type in triggering neuronal apoptosis. Moreover, upregulation of NADPH prevented Dronc-mediated apoptosis upon abrogation of <italic>Drosophila</italic> Inhibitor of Apoptosis (IAP) protein 1 (DIAP1) by double-stranded RNA (dsRNA) or cycloheximide (CHX) treatment, revealing a novel mechanism of DIAP1-independent apoptotic regulation in <italic>Drosophila</italic>. Mechanistically, the CaMKII-mediated phosphorylation of Dronc hindered its activation, but not its catalytic activity. As NADPH levels have been implicated in the regulation of oocyte death, we demonstrate here that a conserved regulatory circuit also coordinates somatic apoptosis and NADPH levels in <italic>Drosophila</italic>.</p><p>Given the regulatory role of NADPH in the activation of Dronc in <italic>Drosophila</italic> and caspase-2 in vertebrates, we then attempted to further elucidate the underlying signaling pathways. By tracking the catabolic fate of NADPH, we revealed that fatty acid synthase (FASN) activity was required for the metabolic suppression of Dronc, as both the chemical inhibitor orlistat and FASN dsRNA abrogated NADPH-mediated protection against CHX-induced apoptosis in S2 cells. Interestingly, it has been previously demonstrated that blocking FASN induces cell death in numerous cancers, including ovarian cancer; however, the mechanism is still obscure. As our results predict that suppression of FASN activity may prevent the inhibitory phosphorylation of Dronc and caspase 2 (at S130 and S164 respectively), we examined the contribution of caspase-2 to cell death induced by orlistat using ovarian cancer cells. Indeed, caspase-2 S164 was dephosphorylated upon orlistat treatment, initiating the cleavage and activation of caspase-2 and its downstream target, Bid. Knockdown of caspase-2 significantly alleviated orlistat-induced cell death, further illustrating its involvement.</p><p>Lastly, we developed an assay based on bimolecular fluorescence complementation (BiFC) to monitor the oligomerization of Dronc in S2 cells, a crucial step in its activation. The sensitivity of this assay has been validated with several apoptotic stimuli. A future whole-genome screen employing this assay is planned to provide new insights into this complex apoptotic regulatory network by unbiasedly identifying novel apoptotic regulators.</p> / Dissertation