Pyridine nucleotide levels in Dictyostelium discoideum during differentiation

Dissecting the function of Atg1 complex in Dictyostelium autophagy reveals a connection with the pentose phosphate pathway enzyme transketolase

The network of protein–protein interactions of the Dictyostelium discoideum autophagy pathway was investigated by yeast two-hybrid screening of the conserved autophagic proteins Atg1 and Atg8. These analyses confirmed expected interactions described in other organisms and also identified novel interactors that highlight the complexity of autophagy regulation. The Atg1 kinase complex, an essential regulator of autophagy, was investigated in detail here. The composition of the Atg1 complex in D. discoideum is more similar to mammalian cells than to Saccharomyces cerevisiae as, besides Atg13, it contains Atg101, a protein not conserved in this yeast. We found that Atg101 interacts with Atg13 and genetic disruption of these proteins in Dictyostelium leads to an early block in autophagy, although the severity of the developmental phenotype and the degree of autophagic block is higher in Atg13-deficient cells. We have also identified a protein containing zinc-finger B-box and FNIP motifs that interacts with Atg101. Disruption of this protein increases autophagic flux, suggesting that it functions as a negative regulator of Atg101. We also describe the interaction of Atg1 kinase with the pentose phosphate pathway enzyme transketolase (TKT). We found changes in the activity of endogenous TKT activity in strains lacking or overexpressing Atg1, suggesting the presence of an unsuspected regulatory pathway between autophagy and the pentose phosphate pathway in Dictyostelium that seems to be conserved in mammalian cells.

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.

Protein-bound mono(ADP-ribose) residues in differentiating cells of Dictyostelium discoideum

Changes in protein-bound mono(ADP-ribose) residues during development of Dictyostelium discoideum were determined. NAD(H) levels and the amounts of the NH2OH resistant and sensitive subfractions of mono(ADPR) were found not to be different between exponentially growing and aggregation-competent cells in which mitosis had ceased. Divergent changes occurred at the differentiation stages following aggregation as indicated by an increase in the ratio of these subfractions from approx. 1 during the growth plase and aggregation competent stage to 2 in the grex, a stage which follows cell aggregation. The fraction of NH2OH sensitive conjugates closely followed the changes in total cellular protein, while the NH2OH resistant ADPR protein conjugates, when based on protein, increased during the stages following aggregation. NAD(H) and NADP(H) levels per unit DNA decreased significantly during this period. The mono(ADPR) to DNA ratio in D. discoideum is comparable to that in proliferating Physarum polycephalum and to non-proliferating adult rat liver. The total amount of mono(ADPR) residues per nucleus is, however, approximately 70-fold higher in the liver, indicating that the quantity of mono(ADPR) residues is more closely related to the size of the eukaryotic genome than to cell proliferation.

Determination by radioimmunoassay of the sum of oxidized and reduced forms of NAD and NADP in picomole quantities from the same acid extract

The sum of the amounts of NAD + NADH was determined from the same acid tissue extract with the aid of a highly specific radioimmunoassay for 5'-AMP. NAD was converted to 5'-AMP via ADP-ribose by alkaline treatment while NADH was converted first to ADP-ribose by incubation of the acid extract at 25 degrees C followed by alkaline conversion to 5'-AMP. Removal of phosphate groups in NADP and NADPH by treatment of the extracts with alkaline phosphatase extended the procedure to the quantification of NADP(H). When combined with enzymic analyses of the oxidized coenzyme forms, NAD/NADH and NADP/NADPH ratios could also be obtained from the same extracts. The sensitivity of the test allows quantification of pyridine nucleotides in the range of 0.1--10 pmol.