Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution

A new method for the mathematical analysis of large metabolic networks is presented. Based on the fact that the occurrence of a metabolic reaction generally requires the existence of other reactions providing its substrates, series of metabolic networks are constructed. In each step of the corresponding expansion process those reactions are incorporated whose substrates are made available by the networks of the previous generations. The method is applied to the set of all metabolic reactions included in the KEGG database. Starting with one or more seed compounds, the expansion results in a final network whose compounds define the scope of the seed. Scopes of all metabolic compounds are calculated and it is shown that large parts of cellular metabolism can be considered as the combined scope of simple building blocks. Analyses of various expansion processes reveal crucial metabolites whose incorporation allows for the increase in network complexity. Among these metabolites are common cofactors such as NAD⁺, ATP, and coenzyme A. We demonstrate that the outcome of network expansion is in general very robust against elimination of single or few reactions. There exist, however, crucial reactions whose elimination results in a dramatic reduction of scope sizes. It is hypothesized that the expansion process displays characteristics of the evolution of metabolism such as the temporal order of the emergence of metabolic pathways. [Reviewing Editor : Dr. David Pollock]     

Challenging the concept of "recycling" as a mechanism for the evolution of homochirality in chemical reactions

The concept that "recycling" of reactants may be key to the spontaneous generation of a homochiral state in closed autocatalytic reaction networks has recently been introduced and has been supported by computer simulations of such reaction networks. It has been suggested that unidirectional cycles maintained away from equilibrium may avoid the inevitable establishment of a racemic state, and under such conditions the explicit reverse reactions dictated by microscopic reversibility may be all be treated as having negligible rates. We show here that because the equilibrium constants in a recycled network are interdependent, it is not valid to neglect all reverse reactions simultaneously; a very low value for the rate constant of one reverse reaction in the network dictates that another reverse reaction in the same network will exhibit a large rate constant. This conclusion is general and applies to any closed mass system where the energy input is subject to microscopic reversibility. Therefore, chemical reversibility cannot be invoked as a mechanism for the evolution of a single chiral molecular state in thermally activated reactions.     

The reconstruction and analysis of tissue specific human metabolic networks

Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liver have already been studied, a systematic study of tissue specific metabolic networks for all main tissues is still missing. In this work, we reconstruct the tissue specific metabolic networks for 15 main tissues in human based on the previously reconstructed Edinburgh Human Metabolic Network (EHMN). The tissue information is firstly obtained for enzymes from Human Protein Reference Database (HPRD) and UniprotKB databases and transfers to reactions through the enzyme-reaction relationships in EHMN. As our knowledge of tissue distribution of proteins is still very limited, we replenish the tissue information of the metabolic network based on network connectivity analysis and thorough examination of the literature. Finally, about 80% of proteins and reactions in EHMN are determined to be in at least one of the 15 tissues. To validate the quality of the tissue specific network, the brain specific metabolic network is taken as an example for functional module analysis and the results reveal that the function of the brain metabolic network is closely related with its function as the centre of the human nervous system. The tissue specific human metabolic networks are available at .     

Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm.

The design of metabolic pathways is thought to be the result of an optimization process such that the structure of contemporary metabolic routes maximizes a particular objective function. Recently, it has been shown that some essential stoichiometric properties of glycolysis can be explained on the basis of the requirement for a high ATP production rate. Because the number of stoichiometrically feasible designs increases strongly with the number of reactions involved, a systematic analysis of all the possibilities turns out to be inaccessible beyond a certain system size. We present, therefore, an alternative approach to compute in a more efficient way the optimal design of glycolysis interacting with an external ATP-consuming reaction. The algorithm is based on the laws of evolution by natural selection, and may be viewed as a particular version of evolutionary algorithms. The following conclusions are derived: (a) evolutionary algorithms are very useful search strategies in determining optimal stoichiometries of metabolic pathways. (b) Essential topological features of the glycolytic network may be explained on the basis of flux optimization. (c) There is a strong interrelation between the optimal stoichiometries and the thermodynamic and kinetic properties of the participating reactions. (d) Some subsequences of reactions in optimal pathways are strongly conserved at variation of system parameters, which may be understood by applying principles of metabolic control analysis.     

RuleMonkey: software for stochastic simulation of rule-based models

Background  

The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems.     

Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments

A computational procedure for identifying the minimal set of metabolic reactions capable of supporting various growth rates on different substrates is introduced and applied to a flux balance model of the Escherichia coli metabolic network. This task is posed mathematically as a generalized network optimization problem. The minimal reaction sets capable of supporting specified growth rates are determined for two different uptake conditions: (i) limiting the uptake of organic material to a single organic component (e.g., glucose or acetate) and (ii) allowing the importation of any metabolite with available cellular transport reactions. We find that minimal reaction network sets are highly dependent on the uptake environment and the growth requirements imposed on the network. Specifically, we predict that the E. coli network, as described by the flux balance model, requires 224 metabolic reactions to support growth on a glucose-only medium and 229 for an acetate-only medium, while only 122 reactions enable growth on a specially engineered growth medium.     

Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis

A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was carried out using a new semi-automated reverse engineering algorithm. The network consists of 422 intracellular metabolites involved in 552 reactions and includes 80 membrane transport reactions. The metabolic network illustrates the reliance of clostridia on the urea cycle, intracellular L-glutamate solute pools, and the acetylornithine transaminase for amino acid biosynthesis from the 2-oxoglutarate precursor. The semi-automated reverse engineering algorithm identified discrepancies in reaction network databases that are major obstacles for fully automated network-building algorithms. The proposed semi-automated approach allowed for the conservation of unique clostridial metabolic pathways, such as an incomplete TCA cycle. A thermodynamic analysis was used to determine the physiological conditions under which proposed pathways (e.g., reverse partial TCA cycle and reverse arginine biosynthesis pathway) are feasible. The reconstructed metabolic network was used to create a genome-scale model that correctly characterized the butyrate kinase knock-out and the asolventogenic M5 pSOL1 megaplasmid degenerate strains. Systematic gene knock-out simulations were performed to identify a set of genes encoding clostridial enzymes essential for growth in silico.     

Biotin amplification of biotin and horseradish peroxidase signals in histochemical stains.

A procedure is described for intensifying histochemical reactions by amplification of biotinylated sites. This is achieved by deposition of biotinylated tyramine on the tissue through the enzymatic action of horseradish peroxidase (HRP). The amplified biotin sites are subsequently visualized by binding them to avidin, to which a marker is attached. This amplification greatly increases the sensitivity of staining procedures that employ HRP (and/or biotin) in tissue. For neuroanatomical pathway tracing methods, the procedure greatly increases the detectability of the injected tracer. For lectin histochemistry and immunohistochemistry, the amplification requires that the lectin or primary antibody be greatly diluted. This dilution results in less background staining and yet strong signals are produced even when very dilute reagents are used. Alternatively, the amplification permits much shorter incubations in primary antibodies when dilutions are used that would ordinarily be used with conventional bridge techniques. The procedure is also useful for amplifying very weak signals, such as those of immunoreactions in glutaraldehyde-fixed tissue. The amplification procedure, together with the availability of avidin probes labeled with fluorochromes, colloidal gold, or enzyme systems other than HRP, provides a means of greatly increasing the versatility of a variety of histochemical reactions, including those for detecting in situ hybridization probes, in addition to increasing the sensitivity of the reactions.     

Time hierarchy, equilibrium and non-equilibrium in metabolic systems.

A metabolic system consists of cooperating biochemical reactions. The motion is described by differential equations in the metabolites. The right-hand sides of these equations are linear combinations of the velocities of the individual reactions. These velocities depend in a non-linear manner on the metabolite concentrations (according to the law of mass action). A characteristic "metabolic" time may be defined for the motion of the whole system. It scales the essential metabolic events whose evolution time is comparable to this metabolite time unit. The constituent reactions of the metabolic system have an individual characteristic time which need not coincide with the general metabolic time. The individual time characterises the approach to the individual equilibrium of the isolated undisturbed reaction. According to the ratio of these two time scales, a single reaction may be fast, or slow, or essential, as compared with the metabolic events. Characteristic time of a single reaction and its steady-state deviation from equilibrium are closely related. It can be shown that the relative deviation from equilibrium of a reaction within the metabolic network is of the same numerical order as the ratio between individual time to metabolic time. The interaction of many reactions with different characteristic times introduces a time hierarchy into the system. This can be made transparent by appropriate scaling and by linear transformation of the system. The subsystem of fast cooperating reactions (dehydrogenases, phosphotransferases) attains a state which is near to the individual equilibrium and reestablishes this state after perturbation. The equilibration is fast; an ultrarapid phase of cofactor equilibrium can be distinguished from the fast phase of substrate equilibrium (exchange of metabolic material between different pathways). During the slower metabolic phase these near-equilibria manifest themselves as stoichiometric linkage between unrelated metabolites. The latter cease to be independent variables and combine to metabolic pools. It can be strictly shown that the essential variables at the metabolic time scale are carrier pools and the degree of occupancy of these carriers by metabolic groups. Chemically different types of carrier pools may be functionally linked together by fast reactions. A consequence of such an arrangement of reactions are distance effects: Changes at one end of a metabolic map may be directly conveyed to other pathways via stoichiometric linkage brought about by fast equilibration of cofactor reactions.     

Reconstruction of the central carbon metabolism of Aspergillus niger.

The topology of central carbon metabolism of Aspergillus niger was identified and the metabolic network reconstructed, by integrating genomic, biochemical and physiological information available for this microorganism and other related fungi. The reconstructed network may serve as a valuable database for annotation of genes identified in future genome sequencing projects on aspergilli. Based on the metabolic reconstruction, a stoichiometric model was set up that includes 284 metabolites and 335 reactions, of which 268 represent biochemical conversions and 67 represent transport processes between the different intracellular compartments and between the cell and the extracellular medium. The stoichiometry of the metabolic reactions was used in combination with biosynthetic requirements for growth and pseudo-steady state mass balances over intracellular metabolites for the quantification of metabolic fluxes using metabolite balancing. This framework was employed to perform an in silico characterisation of the phenotypic behaviour of A. niger grown on different carbon sources. The effects on growth of single reaction deletions were assessed and essential biochemical reactions were identified for different carbon sources. Furthermore, application of the stoichiometric model for assessing the metabolic capabilities of A. niger to produce metabolites was evaluated by using succinate production as a case study.     

Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems

The structural design of ATP and NADH producing systems, such as glycolysis and the citric acid cycle (TCA), is analysed using optimization principles. It is assumed that these pathways combined with oxidative phosphorylation have reached, during their evolution, a high efficiency with respect to ATP production rates. On the basis of kinetic and thermodynamic principles, conclusions are derived concerning the optimal stoichiometry of such pathways. Extending previous investigations, both the concentrations of adenine nucleotides as well as nicotinamide adenine dinucleotides are considered variable quantities. This implies the consideration of the interaction of an ATP and NADH producing system, an ATP consuming system, a system coupling NADH consumption with ATP production and a system consuming NADH decoupled from ATP production. It is examined in what respect real metabolic pathways can be considered optimal by studying a large number of alternative pathways. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations. In this manner, the steady-state ATP production rate can be calculated for any possible ATP and NADH producing pathway. It is shown that most of the possible pathways result in a very low ATP production rate and that the very efficient pathways share common structural properties. Optimization with respect to the ATP production rate is performed by an evolutionary algorithm. The following results of our analysis are in close correspondence to the real design of glycolysis and the TCA cycle. (1) In all efficient pathways the ATP consuming reactions are located near the beginning. (2) In all efficient pathways NADH producing reactions as well as ATP producing reactions are located near the end. (3) The number of NADH molecules produced by the consumption of one energy-rich molecule (glucose) amounts to four in all efficient pathways. A distance measure and a measure for the internal ordering of reactions are introduced to study differences and similarities in the stoichiometries of metabolic pathways.     

The contents of adenine nucleotides, phosphagens and some glycolytic intermediates in resting muscles from vertebrates and invertebrates.

The lowest contents of ATP and the lowest ATP/AMP concentration ratios are observed in the molluscan muscles that have very low rates of energy expenditure during contraction. The highest contents of ATP are observed in the extremely aerobic insect flight muscle and the extremely anaerobic pectoral muscle of the pheasant and domestic fowl. In general, the lowest ATP/AMP concentration ratios are observed for muscle in which the variation in the rate of energy utilization is small (e.g. some molluscan muscles, heart muscle); the highest ratios are observed in muscles in which this variation is large (lobster abdominal muscle, pheasant pectoral muscle, some insect flight muscles). This finding is consistent with the proposed role of AMP and the adenylate kinase reaction in the regulation of glycolysis. However, in the flight muscle of the honey-bee the ATP/AMP ratio is very low, so that glycolysis may be regulated by factors other than the variation in AMP concentration. The variation in the contents of arginine phosphate in muscle from the invertebrates is much larger than the variation in creatine phosphate in muscle from the vertebrates. The contents of hexose monophosphates and pyruvate are, in general, higher in the muscles of vertebrates than in those of the invertebrates. The contents of phosphoenolpyruvate are similar in all the muscles investigated, except for the honey-bee in which it is about 4-10-fold higher. The mass-action ratios for the reactions catalysed by phosphoglucoisomerase and adenylate kinase are very similar to the equilibrium constants for these reactions. Further, the variation in the mass-action ratios between muscles is small. It is concluded that these enzymes catalyse reactions close to equilibrium. However, the mass-action ratios for the reactions catalysed by phosphofructokinase and pyruvate kinase are much smaller than the equilibrium constants. The variation in the ratios between different muscles is large. It is concluded that these enzymes catalyse nonequilibrium reactions. Since the variation in the mass-action ratios for the reactions catalysed by the phosphagen kinases (i.e. creatine and arginine phosphokinases) is small, it is suggested that these reactions are close to equilibrium.     

Prediction of Michaelis-Menten constant of beta-glucosidases using nitrophenyl-beta-D-glucopyranoside as substrate

In this study, we attempted to use the neural network to model a quantitative structure-K(m) (Michaelis-Menten constant) relationship for beta-glucosidase, which is an important enzyme to cut the beta-bond linkage in glucose while K(m) is a very important parameter in enzymatic reactions. Eight feedforward backpropagation neural networks with different layers and neurons were applied for the development of predictive model, and twenty-five different features of amino acids were chosen as predictors one by one. The results show that the 20-1 feedforward backpropagation neural network can serve as a predictive model while the normalized polarizability index as well as the amino-acid distribution probability can serve as the predictors. This study threw lights on the possibility of predicting the K(m) in beta-glucosidases based on their amino-acid features.     

Thymectomy-induced deterioration of learning and memory.

Age-associated immunodeficiency and cognitive deterioration are two predominant features of the aging process, but the mutual influences between them are not clear yet. Research on the neuroendocrine immunomodulation (NIM) network indicate reciprocal interactions between the neuroendocrine and the immune systems mediated by neurotransmitters, neuropeptides, hormones and cytokines, which form an integrated network to maintain normal physiological functions of the body. An imbalance in the NIM network is believed to accelerate the aging process, in which the thymus plays an important role. We recently discovered that thymectomy in mice not only reduces the immune response, but also deteriorates learning performances. Cytokines such as interleukin-1, interleukin-6 and tumor necrosis factor, and corticosterone affect the induction of hippocampal long-term potentiation, a synaptic model of memory. Clinical studies have demonstrated that Alzheimer's patients show disordered immune function in addition to cognitive deficit, and the brain lesions of Alzheimer's patients may be associated with abnormal immune reactions occurring in the brain. With these findings, it is speculated that the disordered immune function may induce an imbalance in the NIM network, which consequently influences central cognitive function.     

Sequence-targeted chemical modifications of nucleic acids by complementary oligonucleotides covalently linked to porphyrins.

Oligo-heptathymidylates covalently linked to porphyrins bind to complementary sequences and can induce local damages on the target molecule. In dark reactions, iron porphyrin derivatives exhibited various chemical reactivities resulting in base oxidation, crosslinking and chain scission reactions. Reactions induced by reductants, such as ascorbic acid, dithiothreitol or mercapto-propionic acid, led to very localised reactions. A single base was the target for more than 50% of the damages. Oxidising agents such as H2O2 and its alkyl derivatives induced reactions that extended to a wider range of altered bases. The specificity of the chemical modifications observed in these systems is discussed from a mechanistic point of view.     

Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition

Background  

Metabolic pathway is a highly regulated network consisting of many metabolic reactions involving substrates, enzymes, and products, where substrates can be transformed into products with particular catalytic enzymes. Since experimental determination of the network of substrate-enzyme-product triad (whether the substrate can be transformed into the product with a given enzyme) is both time-consuming and expensive, it would be very useful to develop a computational approach for predicting the network of substrate-enzyme-product triads.     

Recycling,reproduction, and life's origins

Kinetic considerations make it most improbable that any reproducing system could arise spontaneously in a prebiotic soup containing a large variety of organic molecules, as commonly postulated. This batch process can be contrasted with a completely recycling network of reactions maintained by an influx of energy. So long as the network includes at least two bimolecular reactions it is likely to support pathways for chemical reproduction. However, such reproducing systems will be simple in both kinetic and structural terms. Subsequent evolution will lead to much more complex reproducing structures although the kinetic complexities, measuring the varieties of reactions between these structures and their media, will remain relatively simple.