A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction

The cholesterol biosynthesis pathway has recently been shown to play an important role in the innate immune response to viral infection with host protection occurring through a coordinate down regulation of the enzymes catalysing each metabolic step. In contrast, statin based drugs, which form the principle pharmaceutical agents for decreasing the activity of this pathway, target a single enzyme. Here, we build an ordinary differential equation model of the cholesterol biosynthesis pathway in order to investigate how the two regulatory strategies impact upon the behaviour of the pathway. We employ a modest set of assumptions: that the pathway operates away from saturation, that each metabolite is involved in multiple cellular interactions and that mRNA levels reflect enzyme concentrations. Using data taken from primary bone marrow derived macrophage cells infected with murine cytomegalovirus or treated with IFNγ, we show that, under these assumptions, coordinate down-regulation of enzyme activity imparts a graduated reduction in flux along the pathway. In contrast, modelling a statin-like treatment that achieves the same degree of down-regulation in cholesterol production, we show that this delivers a step change in flux along the pathway. The graduated reduction mediated by physiological coordinate regulation of multiple enzymes supports a mechanism that allows a greater level of specificity, altering cholesterol levels with less impact upon interactions branching from the pathway, than pharmacological step reductions. We argue that coordinate regulation is likely to show a long-term evolutionary advantage over single enzyme regulation. Finally, the results from our models have implications for future pharmaceutical therapies intended to target cholesterol production with greater specificity and fewer off target effects, suggesting that this can be achieved by mimicking the coordinated down-regulation observed in immunological responses.     

Theoretical studies on the regulation of oxidative phosphorylation in intact tissues

The theoretical studies on the regulation of oxidative phosphorylation that were performed with the aid of kinetic models of this process are overviewed. A definition of the regulation of the flux through a metabolic pathway is proposed and opposed to the control exerted by particular enzymes over this flux. Different kinetic models of oxidative phosphorylation proposed in the literature are presented, of which only the model proposed by myself and co-workers was extensively used in theoretical studies on the regulation and compensation in the oxidative phosphorylation system. These theoretical studies have led to the following conclusions: (1) in isolated mitochondria, an increase in the activity of an artificial ATP-using system stimulates mitochondria mainly via changes in [ADP], while changes in [ATP] and [P(i)] play only a minor role; (2) in non-excitable tissues (e.g. liver), hormones (acting via some cytosolic factor(s)) activate directly both ATP usage and at least some enzymes of the ATP-producing block; (3) in excitable tissues (e.g. skeletal muscle), neural signals stimulate (via some cytosolic factor(s)) in parallel all the steps of oxidative phosphorylation together with ATP usage and substrate dehydrogenation; (4) the decrease in the flux through cytochrome oxidase caused by a decrease in oxygen concentration is, at least partially, compensated by a decrease in Delta p and increase in the reduction level of cytochrome c. A theoretical prediction is formulated that there should exist and be observable a universal cytosolic factor/regulatory mechanism which directly activates (at least in excitable tissues) all complexes of oxidative phosphorylation during an increased energy demand.     

Effect of enzyme deficiencies on oxidative phosphorylation: from isolated mitochondria to intact tissues. Theoretical studies

The present article briefly summarizes the theoretical studies made by the authors and co-workers on the effect of inborn enzyme deficiencies on oxidative phosphorylation in intact tissues and on the genesis of mitochondrial diseases. The dynamic computer model of oxidative phosphorylation developed previously allowed to extrapolate experimental data (especially: threshold curves describing the dependence of oxygen consumption and ATP turnover on activities/concentrations of particular oxidative phosphorylation enzymes) obtained for isolated muscle mitochondria in state 3 at saturating oxygen concentrations to more physiological conditions prevailing in intact tissues. In particular, theoretical studies demonstrated that the threshold value of the relative activity/concentration of a given mitochondrial complex, below which a significant decrease in the respiration rate takes place, increases with an increase in energy demand. This fact was proposed as a possible explanation of the tissue specificity of mitochondrial diseases. Additionally, a decreased oxygen concentration was shown to increase the threshold value (and flux control coefficient) for cytochrome oxidase. We subsequently developed a model called binary mitochondria heteroplasmy, in which there are only two subpopulations of mitochondria: one wild-type and one containing only defected molecules of a given enzyme. In this model we show that a defect has a pronounced effect on oxidative phosphorylation, significantly increasing the threshold value. It was also proposed that a parallel activation in the ATP supply-demand system during an increased energy demand significantly lessens the effect of enzyme deficiencies on oxidative phosphorylation (decreases the threshold value). Finally, the necessity of substrate activation may lead to an instability in the system and to appearance of a second threshold, below which respiration suddenly drops to zero, which is equivalent to the energetic death of a cell.     

Effect of the MAPK cascade structure, nuclear translocation and regulation of transcription factors on gene expression

The mitogen activated protein kinase (MAP kinase) cascade system represents a highly conserved prototype of signal transduction by enzyme cascades. One of the best-studied properties of the MAPK system is its ability to convert graded input stimulus to switch-like all-or-none responses. Previous theoretical studies have centered on quantifying dual phosphorylated MAPK as a final output response and have not incorporated its influence on the regulation of gene expression. The main objective of the current work is to understand the regulatory effect of positive feedback loop embedded in the MAPK cascade, nuclear translocation of active MAPK, phosphorylation and activation of nuclear target proteins on the regulation of specific gene expression. To achieve this objective, we have simulated the MAPK cascade system, which resembles Hog1p activation pathway in yeast, at steady state. Thus, the input signal to the MAPK system is correlated with gene expression as a final system-level output response. The steady state simulation results suggest that other than regulating the signal propagation through cascades, the nuclear translocation of activated MAPK and subsequent regulation of gene expression represent one of the key modes to control the threshold level of response. This work proposes that, it is essential to consider the compartmental distributions of signaling species and the corresponding regulatory mechanisms of gene expression to study the system-level performance of signaling modules such as the MAPK cascade. Such an analysis will relate the extracellular cues to the final phenotypic response by capturing the mechanistic details of the signaling pathway.     

Dynamical analysis of cellular networks based on the Green's function matrix

The complexity of cellular networks often limits human intuition in understanding functional regulations in a cell from static network diagrams. To this end, mathematical models of ordinary differential equations (ODEs) have commonly been used to simulate dynamical behavior of cellular networks, to which a quantitative model analysis can be applied in order to gain biological insights. In this paper, we introduce a dynamical analysis based on the use of Green's function matrix (GFM) as sensitivity coefficients with respect to initial concentrations. In contrast to the classical (parametric) sensitivity analysis, the GFM analysis gives a dynamical, molecule-by-molecule insight on how system behavior is accomplished and complementarily how (impulse) signal propagates through the network. The knowledge gained will have application from model reduction and validation to drug discovery research in identifying potential drug targets, studying drug efficacy and specificity, and optimizing drug dosing and timing. The efficacy of the method is demonstrated through applications to common network motifs and a Fas-induced programmed cell death model in Jurkat T cell line.     

Mutations affecting regulation of the anabolic argF and the catabolic aru genes in Pseudomonas aeruginosa PAO

Summary The nucleotide sequence required for a fully functional promoter and operator of the Pseudomonas aeruginosa argF gene (argF _po), the arginine-repressible gene for anabolic ornithine carbamoyltransferase, was defined within a 160 by region. The streptomycin (Sm) resistance genes strAB of plasmid RSF1010 were fused to argF _po. This construct in P. aeruginosa strain PAO conferred resistance to Sm. Mutants of strain PAO were selected which were resistant to Sm in the presence of arginine due to constitutive expression of argF _po —strAB. These mutants were designated argR. They were unable to grow or grew poorly on arginine or ornithine as the sole carbon and nitrogen source. This growth defect (Aru^–/Oru^– phenotype) was correlated with a reduced level of N-succinylornithine aminotransferase, an enzyme participating in the major aerobic pathway for arginine and ornithine catabolism in this organism. The argR mutants were classified into four groups by transduction analysis and three argR mutations were mapped on the PAO chromosome. argR9901 and argR9902 were co-transducible with car-9 (at 1 min) and thus close to the oru-310 locus; argR9906 was localized in the oruI (=aru) gene cluster (67 min). Some aru mutants, which have been isolated previously and which produce very low amounts of all enzymes in the arginine succinyltransferase pathway, were unable to repress the argF gene in an arginine medium. Thus, P. aeruginosa PAO appears to have multiple genes that are involved in the regulation of both the anabolic argF and the catabolic aru genes.Abbreviations Arg^– arginine auxotrophy - Aru arginine utilization - Oru ornithine utilization     

Biochemical and functional studies on the regulation of the Saccharomyces cerevisiae AMPK homolog SNF1

AMP-activated protein kinase (AMPK) is a master metabolic regulator for controlling cellular energy homeostasis. Its homolog in yeast, SNF1, is activated in response to glucose depletion and other stresses. The catalytic (α) subunit of AMPK/SNF1, Snf1 in yeast, contains a protein Ser/Thr kinase domain (KD), an auto-inhibitory domain (AID), and a region that mediates interactions with the two regulatory (β and γ) subunits. Previous studies suggested that Snf1 contains an additional segment, a regulatory sequence (RS, corresponding to residues 392-518), which may also have an important role in regulating the activity of the enzyme. The crystal structure of the heterotrimer core of Saccharomyces cerevisiae SNF1 showed interactions between a part of the RS (residues 460-498) and the γ subunit Snf4. Here we report biochemical and functional studies on the regulation of SNF1 by the RS. GST pulldown experiments demonstrate strong and direct interactions between residues 450-500 of the RS and the heterotrimer core, and single-site mutations in the RS-Snf4 interface can greatly reduce these interactions in vitro. On the other hand, functional studies appear to show only small effects of the RS-Snf4 interactions on the activity of SNF1 in vivo. This suggests that residues 450-500 may be constitutively associated with Snf4, and the remaining segments of the RS, as well as the AID, may be involved in regulating SNF1 activity.     

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

The aspartate‐derived amino‐acid pathway from plants is well suited for analysing the function of the allosteric network of interactions in branched pathways. For this purpose, a detailed kinetic model of the system in the plant model Arabidopsis was constructed on the basis of in vitro kinetic measurements. The data, assembled into a mathematical model, reproduce in vivo measurements and also provide non‐intuitive predictions. A crucial result is the identification of allosteric interactions whose function is not to couple demand and supply but to maintain a high independence between fluxes in competing pathways. In addition, the model shows that enzyme isoforms are not functionally redundant, because they contribute unequally to the flux and its regulation. Another result is the identification of the threonine concentration as the most sensitive variable in the system, suggesting a regulatory role for threonine at a higher level of integration.     

Regulatory steps of glycolysis during environmental anoxia and muscular work in the cockle,Cardium tuberculatum: control of low and high glycolytic flux

Summary Concentrations of glycolytic intermediates, end products of anaerobic metabolism and the adenylates have been determined in the foot muscle and in the whole soft body tissue of the cockle,Cardium tuberculatum, after anoxic incubation and after the performance of vigorous escape movements. Comparison of the mass action ratios (MAR) with the equilibrium constants (Keq) showed that the reactions catalyzed by glycogen phosphorylase, hexokinase, phosphofructokinase (PFK) and pyruvate kinase (PK) were displaced from equilibrium under all physiological situations investigated.Changes in the levels of the glycolytic intermediates showed that activation of phosphofructokinase is largely responsible for the 100-fold increase of glycolytic flux in the foot muscle during exercise.Analysis of the whole soft body tissue showed that PFK is also involved in reduction of the glycolytic flux during anoxia, but a more pronounced change in the MAR occurs for PK, indicating that PK is strongly inhibited under these conditions.Differences in the regulation of glycolysis in muscular and non-muscular tissues can be related to changes in metabolite levels and to tissue-specific forms of pyruvate kinase with different regulatory properties.     

Kinetic considerations for the regulation of adenosine and deoxyadenosine metabolism in mouse and human tissues based on a thymocyte model

Metabolic regulation at a branch point may be determined primarily by relative enzyme activities and affinity for common substrate. Adenosine and deoxyadenosine are both phosphorylated and deaminated and their metabolism was studied in intact mouse thymocytes. From kinetic considerations of two activities competing for a common substrate, the deamination:phosphorylation ratio, $\text{v}{}^{\mathrm{<mtext>d</mtext>}}\text{v}{}^{\mathrm{<mtext>k</mtext>}}$, at high nucleoside concentration, $\text{[}\text{S}\text{]?∞}$, is equal to $\text{V}{}^{\mathrm{<mtext>d</mtext>}}\text{V}{}^{\mathrm{<mtext>k</mtext>}}$, or 34 and 1090 for adenosine and deoxyadenosine, respectively. At low substrate concentrations, $\text{[}\text{S}\text{]?0}$, $\text{v}{}^{\mathrm{<mtext>d</mtext>}}\text{v}{}^{\mathrm{<mtext>k</mtext>}}$ is equal to $\text{V}{}^{\mathrm{<mtext>d</mtext>}}\text{K}{}^{\mathrm{<mtext>k</mtext>}}{}_{\mathrm{<mtext>m</mtext>}}\text{V}{}^{\mathrm{<mtext>k</mtext>}}\text{K}{}^{\mathrm{<mtext>d</mtext>}}{}_{\mathrm{<mtext>m</mtext>}}$, or 0.7 and 285 for adenosine and deoxyadenosine, respectively. The analysis was extended to other mouse and human tissues by measurement of adenosine kinase, deoxyadenosine kinase and adenosine deaminase activities. All tissues were found to preferentially deaminate deoxyadenosine. Three tissue types were apparent with respect to adenosine metabolism: those which preferentially phosphorylate adenosine at all concentrations, those which switch from phosphorylation to deamination between low and high adenosine concentration and those for which deamination is quantitatively important at all concentrations. Lymphoid tissues are representative of the latter category. The kinetic approach we describe offers a means of predicting nucleoside metabolism over a range of concentration which may be technically difficult to otherwise measure. The phosphorylation of adenosine and deoxyadenosine was also studied in intact thymocytes in the presence of adenosine deaminase inhibitors. The rate of deoxyadenosine phosphorylation was unaffected by coformycin or EHNA, whereas adenosine phosphorylation decreased with increasing substrate concentrations to 18% the rate in the absence of adenosine deaminase inhibitors.     

Analysis of effects of 2,2',5,5'-tetrachlorobiphenyl on the flux control in oxidative phosphorylation system in rat liver mitochondria

Modular kinetic analysis reveals that the environmental pollutant 2,2',5,5'-tetrachlorobiphenyl (2,2',5,5'-TCB) affects a large number of steps in oxidative phosphorylation in rat liver mitochondria. 2,2',5,5'-TCB increases membrane permeability to ions, and inhibits NADH dehydrogenase, cytochrome bc1, cytochrome oxidase (all in the respiratory chain) and ATP-synthase (in the phosphorylation subsystem). Surprisingly, flux control distribution does not change. A kinetic model for oxidative phosphorylation was used to simulate these findings, and it was found that combined large changes in the processes indicated indeed left the flux control largely unchanged. In addition, computational analysis with the model indicated that the adenine nucleotide translocator might be inhibited by 2,2',5,5'-TCB.     

A triangular connection between Cyclin G,PP2A and Akt1 in the regulation of growth and metabolism in Drosophila

Size and weight control is a tightly regulated process, involving the highly conserved Insulin receptor/target of rapamycin (InR/TOR) signaling cascade. We recently identified Cyclin G (CycG) as an important modulator of InR/TOR signaling activity in Drosophila. cycG mutant flies are underweight and show a disturbed fat metabolism resembling TOR mutants. In fact, InR/TOR signaling activity is disturbed in cycG mutants at the level of Akt1, the central kinase linking InR and TORC1. Akt1 is negatively regulated by protein phosphatase PP2A. Notably the binding of the PP2A B′-regulatory subunit Widerborst (Wdb) to Akt1 is differentially regulated in cycG mutants, presumably by a direct interaction of CycG and Wdb. Since the metabolic defects of cycG mutant animals are abrogated by a concomitant loss of Wdb, CycG presumably influences Akt1 activity at the PP2A nexus. Here we show that Well rounded (Wrd), another B' subunit of PP2A in Drosophila, binds CycG similar to Wdb, and that its loss ameliorates some, but not all, of the metabolic defects of cycG mutants. We propose a model, whereby the binding of CycG to a particular B′-regulatory subunit influences the tissue specific activity of PP2A, required for the fine tuning of the InR/TOR signaling cascade in Drosophila.     

On the history of studies on cladoceran taxonomy and morphology,with emphasis on early work and causes of insufficient knowledge of the diversity of the group

The long history of cladoceran morphological andtaxonomic studies beginning in the second halfof the 17th century to nowadays is divided into sevensubsequent periods. Each of them is characterized bydomination of specific trends and a noticeableincrease of the number of taxa described. In spite ofthe multitude of studies the taxonomic diversity ofcladocerans, especially at species level, remain to beinsufficiently known. The history of hydrobiology isbriefly reviewed in order to reveal the causes ofthis insufficient knowledge among which historicalfactors and a long domination of an integral approachto studies of continental water bodies are thought tobe most important.     

A peptide containing residues 26-44 of tau protein impairs mitochondrial oxidative phosphorylation acting at the level of the adenine nucleotide translocator

Having confirmed that adenovirus-mediated overexpression of NH₂-tau fragment lacking the first 25 aminoacids evokes a potent neurotoxic effect, sustained by protracted stimulation of NMDA receptors, in primary neuronal cultures we investigated whether and how chemically synthesized NH₂-derived tau peptides, i.e. NH₂-26-44 and NH₂-1-25 fragments, affect mitochondrial function. We tested both fragments on each step of the processes leading to ATP synthesis via oxidative phosphorylation: i) electron flow via the respiratory chain from physiological substrates to oxygen with the activity of each individual complex of the respiratory chain investigated in some detail, ii) membrane potential generation arising from externally added succinate and iii) the activity of both the adenine nucleotide translocator and iv) ATP synthase. Oxidative phosphorylation is not affected by NH₂-1-25 tau fragment, but dramatically impaired by NH₂-26-44 tau fragment. Both cytochrome c oxidase and the adenine nucleotide translocator are targets of NH₂-26-44 tau fragment, but adenine nucleotide translocator is the unique mitochondrial target responsible for impairment of oxidative phosphorylation by the NH₂-26-44 tau fragment, which then exerts deleterious effects on cellular availability of ATP synthesized into mitochondria.     

Experimental and theoretical studies on the excess capacity of Photosystem II

It has been recently suggested that compensatory changes in Photosystem II (PS II) electron turnover rates can protect photosynthesis from photoinhibition [Behrenfeld et al. (1998) Photosynth Res 58: 259–268]. We have further explored this feature of PS II using a rate electrode for simultaneous measurements of the steady-state rate of oxygen evolution and the oxygen flash yield depending on the background irradiance in both control and photoinhibited algal cells of Chlorella Böhm. Theoretical simulations based on the two-electron gate model agree qualitatively with experimental data if we assume an increase of the electron turnover rate in the remaining functional PS II centers of the photoinhibited sample. Our results confirm the hypothesis that the compensatory effect enables cells to maintain the maximal rates of photosynthesis even in the presence of moderate photoinhibition (decrease of up to 50% in the number of functional centers) and that the effect originates from the inner capacity of electron transport through PS II. The origin of the compensatory effect is briefly discussed.     

Involvement and interaction of various signaling compounds on the plant metabolic events during defense response,resistance to stress factors,formation of secondary metabolites and their molecular aspects

Plants are a nearly unlimited source of phytochemicals. The plants produce various secondary metabolites, which are useful in its interaction with the environment, various stress factors and development of resistance against pathogen attack. A wide array of external stimuli are capable of triggering changes in the plant cell which leads to a cascade of reactions, ultimately resulting in the formation and accumulation of secondary metabolites which helps the plant to overcome the stress factors. The biotic and abiotic elicitors can result in an enhancement of the secondary metabolite production. The stimuli are perceived by receptors, which then result in the activation of the secondary messengers. These then transmit the signals into the cell through the signal transduction pathways leading to gene expression and biochemical changes. There is interplay of the signaling molecules also which regulates the entire pathway. This review is oriented towards the factors, which influence signal transduction pathway(s) with special reference to polyamines, calcium, jasmonates, salicylates, nitric oxide and ethylene. The interplay of these components to elicit a defense response is discussed. Molecular aspects of disease resistance and regulation of plant secondary metabolism has also been presented.     

Cannabidiol as an emergent therapeutic strategy for lessening the impact of inflammation on oxidative stress

Oxidative stress with reactive oxygen species generation is a key weapon in the arsenal of the immune system for fighting invading pathogens and initiating tissue repair. If excessive or unresolved, however, immune-related oxidative stress can initiate further increasing levels of oxidative stress that cause organ damage and dysfunction. Targeting oxidative stress in various diseases therapeutically has proven more problematic than first anticipated given the complexities and perversity of both the underlying disease and the immune response. However, growing evidence suggests that the endocannabinoid system, which includes the CB₁ and CB₂ G-protein-coupled receptors and their endogenous lipid ligands, may be an area that is ripe for therapeutic exploitation. In this context, the related nonpsychotropic cannabinoid cannabidiol, which may interact with the endocannabinoid system but has actions that are distinct, offers promise as a prototype for anti-inflammatory drug development. This review discusses recent studies suggesting that cannabidiol may have utility in treating a number of human diseases and disorders now known to involve activation of the immune system and associated oxidative stress, as a contributor to their etiology and progression. These include rheumatoid arthritis, types 1 and 2 diabetes, atherosclerosis, Alzheimer disease, hypertension, the metabolic syndrome, ischemia-reperfusion injury, depression, and neuropathic pain.