The tricarboxylic acid cycle in Dictyostelium discoideum. Metabolite concentrations, oxygen uptake and 14c-labelled amino acid labelling patterns

Steroids initiate a signaling cascade that triggers rapid sporulation in Dictyostelium

Encapsulation of prespore cells of Dictyostelium discoideum is controlled by several intercellular signals to ensure appropriate timing during fruiting body formation. Acyl-CoA-binding protein, AcbA, is secreted by prespore cells and processed by the prestalk protease TagC to form the 34 amino acid peptide SDF-2 that triggers rapid encapsulation. AcbA is secreted when gamma-aminobutyric acid (GABA) is released from prespore cells and binds to GrlE, a G protein-coupled receptor (GPCR). Analysis of SDF-2 production in mutant strains lacking Galpha subunits and GPCRs, either as pure populations or when mixed with other mutant strains, uncovered the non-cell-autonomous roles of GrlA, Galpha4 and Galpha7. We found that Galpha7 is essential for the response to GABA and is likely to be coupled to GrlE. GrlA-null and Galpha4-null cells respond normally to GABA but fail to secrete it. We found that they are necessary for the response to a small hydrophobic molecule, SDF-3, which is released late in culmination. Pharmacological inhibition of steroidogenesis during development blocked the production of SDF-3. Moreover, the response to SDF-3 could be blocked by the steroid antagonist mifepristone, whereas hydrocortisone and other steroids mimicked the effects of SDF-3 when added in the nanomolar range. It appears that SDF-3 is a steroid that elicits rapid release of GABA by acting through the GPCR GrlA, coupled to G protein containing the Galpha4 subunit. SDF-3 is at the head of the cascade that amplifies the signal for encapsulation to ensure the rapid, synchronous formation of spores.

Kinetic flux profiling for quantitation of cellular metabolic fluxes

This protocol enables quantitation of metabolic fluxes in cultured cells. Measurements are based on the kinetics of cellular incorporation of stable isotope from nutrient into downstream metabolites. At multiple time points, after cells are rapidly switched from unlabeled to isotope-labeled nutrient, metabolism is quenched, metabolites are extracted and the extract is analyzed by chromatography-mass spectrometry. Resulting plots of unlabeled compound versus time follow variants of exponential decay, with the flux equal to the decay rate multiplied by the intracellular metabolite concentration. Because labeling is typically fast (t(1/2)<or=5 min for central metabolites in Escherichia coli), variations on this approach can effectively probe dynamically changing metabolic fluxes. This protocol is exemplified using E. coli and nitrogen labeling, for which quantitative flux data for approximately 15 metabolites can be obtained over 3 d of work. Applications to adherent mammalian cells are also discussed.

Ammonia signaling in yeast colony formation

Multicellular structures formed by microorganisms possess various properties, which make them interesting in terms of processes that occur in tissues of higher eukaryotes. These include processes important for morphogenesis and development of multicellular structures as well as those evoked by stress, starvation, and aging. Investigation of colonies created by simple nonmotile yeast cells revealed the existence of various regulators involved in their development. One of the identified signaling compounds, unprotonated volatile ammonia, is produced by colonies in pulses and seems to represent a long-distance signal notifying the colony population of incoming nutrient starvation. This alarm evokes changes in colonies that are important for their long-term survival. Models of the action of ammonia on yeast cells as well as the routes of its production are proposed. Interestingly, ammonia/ammonium also act as a signaling molecule in other organisms. Ammonia regulates several steps of the multicellular development of Dictyostelium discoideum and evidence indicates that ammonia/ammonium plays a role in neural tissues of higher eukaryotes.

Rapid patterning and zonal differentiation in a two-dimensionalDictyosteliumcell mass: the role of pH and ammonia

Recently it was demonstrated that a rapidly forming, self-organizing pattern that emerges within two-dimensional Dictyostelium discoideumcell cultures could later give rise to stripes of distinct zones, each comprising different cell types. Here we report physiological aspects of the initial rapid patterning and its relationship to cell differentiation. We found that as the temperature is lowered the characteristic length of the pattern increases. From this we estimated the activation energy of the patterning kinetics. Fluorescence of fluorescein-conjugated dextran revealed that the cytosolic pH of cells in the inside zone becomes lower than that in the outer zone facing the air. The patterning could be inhibited by addition of the plasma-membrane proton pump inhibitors diethystilbestrol (DES) or miconazole. Preincubation of cells with weak acid delayed the timing of the patterning, whereas weak base hastened it. A pH-indicating dye revealed localized accumulation of ammonia in the extracellular space. These results suggest that gradients of secreted metabolites may be directly responsible for the rapid patterning and its consequence on cell differentiation in a confined geometrical situation. Possible diffusible candidate molecules and a reaction scheme coupled to the imposed oxygen gradient are discussed.

In vivo stationary flux analysis by 13C labeling experiments

Stationary flux analysis is an invaluable tool for metabolic engineering. In the last years the metabolite balancing technique has become well established in the bioengineering community. On the other hand metabolic tracer experiments using 13C isotopes have long been used for intracellular flux determination. Only recently have both techniques been fully combined to form a considerably more powerful flux analysis method. This paper concentrates on modeling and data analysis for the evaluation of such stationary 13C labeling experiments. After reviewing recent experimental developments, the basic equations for modeling carbon labeling in metabolic systems, i.e. metabolite, carbon label and isotopomer balances, are introduced and discussed in some detail. Then the basics of flux estimation from measured extracellular fluxes combined with carbon labeling data are presented and, finally, this method is illustrated by using an example from C. glutamicum. The main emphasis is on the investigation of the extra information that can be obtained with tracer experiments compared with the metabolite balancing technique alone. As a principal result it is shown that the combined flux analysis method can dispense with some rather doubtful assumptions on energy balancing and that the forward and backward flux rates of bidirectional reaction steps can be simultaneously determined in certain situations. Finally, it is demonstrated that the variant of fractional isotopomer measurement is even more powerful than fractional labeling measurement but requires much higher numerical effort to solve the balance equations.

Evidence for a developmentally regulated prespore-specific glutamine synthetase in the cellular slime mould Dictyostelium discoideum

The enzyme glutamine synthetase (GS) is described for the first time in Dictyostelium discoideum. The appearance of this enzyme is developmentally regulated. The level of activity is low in vegetative cells and increases more than threefold during differentiation. Furthermore this enzyme is shown to be differentially localized in prespore cells, the specific activity being approximately fourfold higher than in prestalk cells. The enzyme has a pH optimum of 7.8 and 8.2 in the gamma-glutamyltransferase and gamma-glutamylsynthetase assays, respectively, and a temperature optimum of 45 degrees C. Kinetic studies of GS revealed apparent Km values of 5.9 mM, 0.009 mM and 8.6 mM for glutamine, ADP and NH2OH, respectively, in the gamma-glutamyltransferase assay, and of 2.2 mM, 0.12 mM and 0.64 mM for glutamate, ATP and NH2OH, respectively, in the gamma-glutamylsynthetase assay.

Developmental decisions in Dictyostelium discoideum

A few hours after the onset of starvation, amoebae of Dictyostelium discoideum start to form multicellular aggregates by chemotaxis to centers that emit periodic cyclic AMP signals. There are two major developmental decisions: first, the aggregates either construct fruiting bodies directly, in a process known as culmination, or they migrate for a period as "slugs." Second, the amoebae differentiate into either prestalk or prespore cells. These are at first randomly distributed within aggregates and then sort out from each other to form polarized structures with the prestalk cells at the apex, before eventually maturing into the stalk cells and spores of fruiting bodies. Developmental gene expression seems to be driven primarily by cyclic AMP signaling between cells, and this review summarizes what is known of the cyclic AMP-based signaling mechanism and of the signal transduction pathways leading from cell surface cyclic AMP receptors to gene expression. Current understanding of the factors controlling the two major developmental choices is emphasized. The weak base ammonia appears to play a key role in preventing culmination by inhibiting activation of cyclic AMP-dependent protein kinase, whereas the prestalk cell-inducing factor DIF-1 is central to the choice of cell differentiation pathway. The mode of action of DIF-1 and of ammonia in the developmental choices is discussed.

The NAD-dependent glutamate dehydrogenase from Dictyostelium discoideum: purification and properties

The NAD-dependent glutamate dehydrogenase (GDH) from Dictyostelium discoideum was purified 1101-fold with a yield of 23.4%. The enzyme has an apparent Mr of 356 kDa, determined using Sephacryl S400, and a subunit molecular weight of 54 kDa on SDS-polyacrylamide gel electrophoresis. The Kms for alpha-ketoglutarate, NADH, and NH4+ are 0.36 +/- 0.03 mM, 16.0 +/- 0.1 microM, and 34.5 +/- 2.7 mM, respectively. The purified enzyme has a pH optimum of pH 7.25-7.5. At 0.1 mM, ADP and AMP stimulate GDH activity 25 and 102%, respectively. Half-maximal activity in the presence of 0.1 mM AMP for alpha-ketoglutarate, NADH, and NH4+ is reached at 2.3 +/- 0.1 mM, 71.4 +/- 5.5 microM, and 27.9 +/- 3.6 mM, respectively.

Construction of kinetic models to understand metabolism in vivo

This review describes increasingly complex kinetic models that simulate carbohydrate metabolism in a simple eucaryotic system which undergoes differentiation. Dynamic models of complex metabolic networks serve to organize and analyze the many interdependent variables involves and to define the rate-limiting events controlling metabolism in vivo. Since the ultimate justification for and test of any model are its predictive values, a series of predictions and related experiments will be described.

Cellular concentrations of enzymes and their substrates

The activity of crude and pure enzyme preparations as well as the molecular weight of these enzymes were obtained from the literature for several organisms. From these data enzyme concentrations were calculated and compared to the concentration(s) of their substrates in the same organism. The data are expressed as molar ratios of metabolite concentration to enzyme site concentration. Of the 140 ratios calculated, 88% were one or greater, indicating that in general substrates exceed their cognate enzyme concentrations. Of the 17 cases where enzyme exceeds metabolite concentration, 16 were in glycolysis. The data in general justify the use of enzyme kinetic mechanisms determined in vitro in the construction of dynamic models which simulate in vivo metabolism.

Pyruvate oxidation in vivo and in vitro in Dictyostelium discoideum

The in vivo rate of the reaction catalyzed by the pyruvate dehydrogenase complex in Dictyostelium discoideum was measured by exposing cells to [1-14C]alanine and relating the rate of 14CO2 evolution to the specific radioactivity of the isolated [1-14C]pyruvate. The rate obtained, 0.33 mumol/min per ml packed cell volume, was very similar to that determined by independent calculations based upon the rate of utilization of endogenous protein as an energy source in this system.

The tricarboxylic acid cycle in Dictyostelium discoideum. A model of the cycle at preculmination and aggregation

A preliminary model of tricarboxylic acid-cycle activity in Dictyostelium discoideum is presented. Specific-radioactivity labelling patterns of intra- and extra-mitochondrial pools are simulated by this model and compared with the experimental data. The model arrived at by this method shows the following features. (1) The cycle flux rate is approx. 0.4 mM/min. (2) Both fumarate and malate are compartmentalized at approx. 1:5 between cycle pools and non-cycle pools. These may represent mitochondrial and cytoplasmic pools. Citrate is compartmentalized at 1:10. Succinate appears to exist in three compartments, two of which become labelled by [14C]glutamate and only one by [14C]aspartate (3) Two pools of aspartate with two associated pools of oxaloacetate are necessary for simulation. (4) Exchange between the cycle and non-cycle pools of both citrate and fumarate occurs at very low rates of about 0.003 mM/min, whereas exchange between the malate pools is about 0.004 mM/min. The exchange reaction glutamate in equilibrium 2-oxoglutarate runs at approx. 15 times the cycle flux. (5) A reaction catalysed by "malic" enzyme is included in the model, as this reaction is necessary for complete oxidation of amino acid substrates. (6) Calculation of the ATP yield from the model is consistent with earlier estimates of ATP turnover if the activity of adenylate kinase is considered.