Detecting and investigating substrate cycles in a genome-scale human metabolic network.

Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described to occur in the muscles of bumblebees and brown adipose tissue in the 1970s. A popular example is the conversion of fructose 6-phosphate to fructose 1,6-bisphosphate and back. In the present study, we analyze a large number of substrate cycles in human metabolism that consume ATP and discuss their statistics. For this purpose, we use two recently published methods (i.e. EFMEvolver and the K-shortest EFM method) to calculate samples of 100,000 and 15,000 substrate cycles, respectively. We find an unexpectedly high number of substrate cycles in human metabolism, with up to 100 reactions per cycle, utilizing reactions from up to six different compartments. An analysis of tissue-specific models of liver and brain metabolism shows that there is selective pressure that acts against the uncontrolled dissipation of energy by avoiding the coexpression of enzymes belonging to the same substrate cycle. This selective force is particularly strong against futile cycles that have a high flux as a result of thermodynamic principles.

NAD(+) biosynthesis and salvage--a phylogenetic perspective.

NAD is best known as an electron carrier and a cosubstrate of various redox reactions. However, over the past 20 years, NAD(+) has been shown to be a key signaling molecule that mediates post-translational protein modifications and serves as precursor of ADP-ribose-containing messenger molecules, which are involved in calcium mobilization. In contrast to its role as a redox carrier, NAD(+)-dependent signaling processes involve the release of nicotinamide (Nam) and require constant replenishment of cellular NAD(+) pools. So far, very little is known about the evolution of NAD(P) synthesis in eukaryotes. In the present study, genes involved in NAD(P) metabolism in 45 species were identified and analyzed with regard to similarities and differences in NAD(P) synthesis. The results show that the Preiss-Handler pathway and NAD(+) kinase are present in all organisms investigated, and thus seem to be ancestral routes. Additionally, two pathways exist that convert Nam to NAD(+); we identified several species that have apparently functional copies of both biosynthetic routes, which have been thought to be mutually exclusive. Furthermore, our findings suggest the parallel phylogenetic appearance of Nam N-methyltransferase, Nam phosphoribosyl transferase, and poly-ADP-ribosyltransferases.

Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach.

Elementary-mode analysis is a powerful method for detecting all potential pathways in a metabolic network and computing the associated molar yields. Metabolic pathways can be interpreted as different strategies of organisms. Thus, methods from Evolutionary Game Theory can be employed. In Flux Balance Analysis (FBA), it is usually assumed that molar yields of relevant products (such as biomass or ATP) have been maximized during evolution. This has been questioned on game-theoretical grounds. In particular, in situations that can be characterized as a Prisoner's Dilemma, maximization of flux is not in line with maximization of yield. Under other conditions (that is, for other parameter values of maximal velocities), a Harmony game can result, where the above two maximization criteria give the same result. Here, we analyse the optimal situations under varying conditions. In particular, we consider the case where the cell can allocate a certain amount of protein on several enzymes in a varying distribution and model this by a linear programming problem in which not only the rates but also the maximal velocities are variable. It turns out that in the case of low or moderate synthesis costs for the enzymes of the high-yield pathway, maximizing pathway flux is in line with maximizing molar yield while in the case of high costs, it is not. This may explain the observation that many cells such as striated muscle cells, tumour cells, activated lymphocytes and several yeasts do not reallocate protein away from glycolytic enzymes towards TCA cycle and respiratory chain enzymes, in spite of the higher efficiency of respiration. This provides a straightforward explanation of the Warburg effect in tumour cells.