Co-ordinate control of phosphofructokinase and pyruvate kinase by fructose diphosphate: a mechanism for amplification and step changes in the regulation of glycolysis in liver

The platelet isoform of phosphofructokinase contributes to metabolic reprogramming and maintains cell proliferation in clear cell renal cell carcinoma

Metabolic alterations underlying clear cell renal cell carcinoma (ccRCC) progression include aerobic glycolysis, increased pentose phosphate pathway activity and reduced oxidative phosphorylation. Phosphofructokinase (PFK), a key enzyme of the glycolytic pathway, has L, M, and P isoforms with different tissue distributions. The mRNA level of the platelet isoform of phosphofructokinase (PFKP) is reported to be up-regulated in ccRCC patients. However, it remains unclear whether PFKP plays an important role in promoting aerobic glycolysis and macromolecular biosynthesis to support cell proliferation in ccRCC. Here we found that the up-regulated PFKP became the predominant isoform of PFK in human ccRCC. Suppression of PFKP not only impaired cell proliferation by inducing cell cycle arrest and apoptosis, but also led to decreased glycolysis, pentose phosphate pathway and nucleotide biosynthesis, accompanied by activated tricarboxylic acid cycle in ccRCC cells. Moreover, we found that p53 activation contributed to cell proliferation and metabolic defects induced by PFKP knockdown in ccRCC cells. Furthermore, suppression of PFKP led to reduced ccRCC tumor growth in vivo. Our data indicate that PFKP not only is required for metabolic reprogramming and maintaining cell proliferation, but also may provide us with a valid target for anti-renal cancer pharmaceutical agents.

Zinc inhibition of pyruvate kinase of M-type isozyme

Inhibitory effect of Zn on the pyruvate kinase of M (muscle)-type isozyme was analyzed for the purpose of elucidating the cytotoxicity of Zn. Zn inhibited pyruvate kinase uncompetitively with respect to the substrate PEP, and competitively with respect to ADP. Quotient velocity plot calculated from the Zn-inhibition curves showed that Zn²⁺ as a ZnADP complex acted as competitive and uncompetitive inhibitors of the enzyme with respect to the substrate ADP and PEP, respectively: Zn²⁺ forms a ZnADP complex, which may bind to the ADP-binding site of the free enzyme with the K_i value of 1.4 μM causing competitive inhibition, or to the ADP-site of the enzyme-PEP complex with 2.6 μM resulting in uncompetitive inhibition. The inhibition of pyruvate kinase by Zn²⁺ may be responsible for the cytotoxicity of this metal by decreasing glycolytic flux.

Effect of fructose 1,6-bisphosphate on the iron redox state relating to the generation of reactive oxygen species

Role of fructose 1,6-bisphosphate-mediated iron oxidation in the generation of reactive oxygen species was analyzed. Aconitase the most sensitive enzyme to oxidative stress was inactivated potently by fructose 1,6-bisphosphate in the presence of ferrous ion, and further by ADP and PEP to a lesser extent. The inactivation requires cyanide, suggesting that the superoxide radical is responsible for the inactivation. Addition of ascorbic acid and dithiothreitol prevented aconitase from the inactivation. Fructose 1,6-bisphosphate, ADP and PEP stimulated the oxidation of ferrous ion causing one-electron reduction of oxygen molecule. Superoxide radical formed with iron oxidation participates in the oxidative inactivation of aconitase and the citric acid cycle, resulting in the induction of the Crabtree effect, that is, high glucose-mediated inhibition of oxidative metabolism in mitochondria.

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.

Iron-dependent oxidative inactivation with affinity cleavage of pyruvate kinase

Treatment of rabbit muscle pyruvate kinase with iron/ascorbate caused an inactivation with the cleavage of peptide bond. The inactivation or fragmentation of the enzyme was prevented by addition of Mg2+, catalase, and mannitol, but ADP and PEP the substrates did not show any effect. Protective effect of catalase and mannitol suggests that hydroxyl radical produced through the ferrous ion-dependent reduction of oxygen is responsible for the inactivation/fragmentation of the enzyme. SDS-PAGE and TOF-MS analysis confirmed five pairs of fragments, which were determined to result from the cleavage of the Lys114-Gly115, Glu117-Ile118, Asp177-Gly178, Gly207-Val208, and Phe243-Ile244 bonds of the enzyme by amino-terminal sequencing analysis. Protection of the enzyme by Mg2+ implies the identical binding sites of Fe2+ and Mg2+, but the cleavage sites were discriminated from the cofactor Mg2+-binding sites. Considering amino acid residues interacting with metal ions and tertiary structure, Fe2+ ion may bind to Asp177 neighboring to Gly207 and Glu117 neighboring to Lys114 and Phe243, causing the peptide cleavage by hydroxyl radical. Iron-dependent oxidative inactivation/fragmentation of pyruvate kinase can explain the decreased glycolytic flux under aerobic conditions. Intracellular free Mg2+ concentrations are responsible for the control of cellular respiration and glycolysis.

Dynamic behavior in glycolytic oscillations with phase shifts

Practically all of the studies of glycolytic oscillations in homogeneous spatial mediums have been performed through the construction of systems of ordinary differential equations and the search for their solutions. In this kind of modelling, the system dynamic behavior is considered to depend only on the values adopted by the parameters related to the dependent variables. In the present work, the modeling of a biochemical system through a system of functional differential equations with delay allows us to analyse the consequences that the variations in the parametric values linked to the independent variable (time) have upon the integral solutions of the system. In our model, the delays correspond with phase shifts in the initial functions for two dependent variables. The results of our researches show that when a instability-generating multienzymatic mechanism suffers variations of the delay time in any of its variables, a wide range of different dynamic responses can be produced. Our work is presented as an enlargement on the dynamic study of biochemical oscillations in general and, particularly, the glycolytic oscillations, under the consideration of the existence of variations in the phase shifts during the oscillations of metabolites involved in the studied reactive processes.

Theoretical analysis of the flux control properties of a substrate cycle

Substrate cycles are able to increase the flux control of a non-equilibrium reaction in a wide range of situations related to the effects of the metabolites involved in the cycle on the reaction producing them. No limit exists for that amplification if appropriate conditions are attained if those effects are positive. In all cases, the ratio between the rate of the reverse reaction and the net flux through the pathway plays an important role in defining the final amplification.

Mathematical modelling of dynamics and control in metabolic networks. V. Static bifurcations in single biochemical control loops

Here we expand an earlier study of feedback activation in simple linear reaction sequences by searching the parameter space of biologically realistic rate laws for multiple stable steady states. The impetus for this work is to seek the origin of decision making strategies at the metabolic level, with particular emphasis on the switching between the operating conditions needed to meet changing substrate availability and organism requirements. The control loop considered herein is a linear reaction chain in which the end product of the reaction sequence feedback activates the first reaction in the sequence to produce feedback control. It has been found that the criteria for the existence of multiple steady state solutions in such loops involve only the kinetics of the regulatory enzyme controlling the first reaction and that of end product removal. The effects of these kinetics are examined here using two representative models for the regulatory enzyme: the lumped controller, based on Hill-type kinetics, and the symmetry model. The behavior of these two models is qualitatively similar, and both show the characteristics needed for switching between low and high substrate utilization. The removal rate is assumed to be of the Michaelis-Menten type. Judicious scaling of the governing equations permits separation of genetically determined kinetic parameters from concentration dependent ones. This allows us to conclude that, for a fixed set of kinetic parameters, the steady state flux through the loop can be switched between stable steady states by merely varying metabolite or enzyme concentrations. In particular, when the initial substrate exceeds a certain critical level, the loop can be "switched on" (by a discontinuous increase in the flux through the chain), and similarly, when it falls below a critical level, the pathway is shut down. Similar effects can be realized by varying the ratios of enzyme concentrations. It is proposed that by identifying these critical points one can gain significant insight into the objectives of decision making at the metabolic level.

Control of liver 6-phosphofructokinase by fructose 2,6-bisphosphate and other effectors

Rat liver 6-phosphofructokinase (ATP-D-fructose-6-phosphate 1-phosphotransferase, EC 2.7.1.11) was partially purified free of interfering enzymes by a rapid procedure. Fructose 2,6-bisphosphate, at micromolar concentrations, greatly stimulated the enzyme by increasing its affinity for fructose 6-phosphate and relieving the inhibition by ATP. Its action was synergistic with that of AMP. As a stimulator of liver phosphofructokinase, fructose 2,6-bisphosphate was approximately 1000- and 2500-fold more efficient than fructose 1,6-bisphosphate and glucose 1,6-bisphosphate, respectively. The concentration at which a half-maximal effect was obtained with the hexose bisphosphates was dependent upon the experimental conditions. It was relatively high at physiological concentrations of substrates, AMP, and Pi, and under these conditions the positive effect of fructose 1,6-bisphosphate was no longer detectable. This was probably due to the negative effect of fructose 1,6-bisphosphate as a reaction product inhibitor. It is concluded that fructose 2,6-bisphosphate rather than fructose 1,6-bisphosphate controls, in association with other effectors, the activity of phosphofructokinase in the liver.