Biomedical subjects

Pedro de Atauri

Publications and source records attributed to Pedro de Atauri.

14 recordsLinked to original sources

PubMed2006

Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.

Transcriptional noise is known to be an important cause of cellular heterogeneity and phenotypic variation. The extent to which molecular interaction networks may have evolved to either filter or exploit transcriptional noise is a much debated question. The yeast genetic network regulating galactose metabolism involves two proteins, Gal3p and Gal80p, that feed back positively and negatively, respectively, on GAL gene expression. Using kinetic modeling and experimental validation, we demonstrate that these feedback interactions together are important for (i) controlling the cell-to-cell variability of GAL gene expression and (ii) ensuring that cells rapidly switch to an induced state for galactose uptake.

Computer Simulation↗

PubMed2005

A data integration methodology for systems biology.

Different experimental technologies measure different aspects of a system and to differing depth and breadth. High-throughput assays have inherently high false-positive and false-negative rates. Moreover, each technology includes systematic biases of a different nature. These differences make network reconstruction from multiple data sets difficult and error-prone. Additionally, because of the rapid rate of progress in biotechnology, there is usually no curated exemplar data set from which one might estimate data integration parameters. To address these concerns, we have developed data integration methods that can handle multiple data sets differing in statistical power, type, size, and network coverage without requiring a curated training data set. Our methodology is general in purpose and may be applied to integrate data from any existing and future technologies. Here we outline our methods and then demonstrate their performance by applying them to simulated data sets. The results show that these methods select true-positive data elements much more accurately than classical approaches. In an accompanying companion paper, we demonstrate the applicability of our approach to biological data. We have integrated our methodology into a free open source software package named POINTILLIST.

Informatics↗

PubMed2005

A data integration methodology for systems biology: experimental verification.

The integration of data from multiple global assays is essential to understanding dynamic spatiotemporal interactions within cells. In a companion paper, we reported a data integration methodology, designated Pointillist, that can handle multiple data types from technologies with different noise characteristics. Here we demonstrate its application to the integration of 18 data sets relating to galactose utilization in yeast. These data include global changes in mRNA and protein abundance, genome-wide protein-DNA interaction data, database information, and computational predictions of protein-DNA and protein-protein interactions. We divided the integration task to determine three network components: key system elements (genes and proteins), protein-protein interactions, and protein-DNA interactions. Results indicate that the reconstructed network efficiently focuses on and recapitulates the known biology of galactose utilization. It also provided new insights, some of which were verified experimentally. The methodology described here, addresses a critical need across all domains of molecular and cell biology, to effectively integrate large and disparate data sets.

Chromatin Immunoprecipitation↗

PubMed2005

Metabolic homeostasis in the human erythrocyte: in silico analysis.

A detailed computer model of human erythrocyte metabolism was shown to predict three steady states, two stable and one unstable. The most extreme steady state is characterized by almost zero concentrations of all the phosphorylated intermediates. The "normal" steady state is remarkably robust in the face of large changes in the activity of most of the enzymes of glycolysis and the pentose phosphate pathway: this steady state can be viewed as an attractor towards which the system returns following a metabolic perturbation. Focus is given to three responses of the system: (1) the 'energy charge' that pertains to the concentration of ATP relative to all purine nucleotides; (2) redox power expressed as the ratio of reduced-to-total glutathione and (3) the concentration of 2,3-bisphosphoglycerate, that directly affects the oxygen affinity of haemoglobin thus affecting the main physiological function of the cell. The collapse of the normal steady state in what can be viewed topologically as a catastrophe is posited as one key element of erythrocyte senescence and it is particularly important for erythrocyte destruction in patients with an inborn enzyme deficiency.

2,3-Diphosphoglycerate↗

PubMed2005

Is the regulation of galactose 1-phosphate tuned against gene expression noise?

The average number of mRNA molecules per active gene in yeast can be remarkably low. Consequently, the relative number of copies of each transcript per cell can vary greatly from moment to moment. When these transcripts are encoding metabolic enzymes, how do the resulting variations in enzyme concentrations affect the regulation of metabolic intermediates? Using a kinetic model of galactose utilization in yeast, we analysed the transmission of noise from transcription and translation on metabolic intermediate regulation. In particular, the effect of the kinetic properties of the galactose-1-phosphate uridylyltransferase reaction on the transmission of noise was analysed.

Galactose↗

PubMed2004

Characterization of the first described mutation of human red blood cell phosphoglycerate mutase.

In a patient with clinical diagnosis of Hereditary Spherocytosis and partial deficiency (50%) of red blood cell phosphoglycerate mutase (PGAM) activity, we have recently reported [A. Repiso, P. Pérez de la Ossa, X. Avilés, B. Oliva, J. Juncá, R. Oliva, E. Garcia, J.L.L. Vives-Corrons, J. Carreras, F. Climent, Red blood cell phosphoglycerate mutase. Description of the first human BB isoenzyme mutation, Haematologica 88 (2003) (03) ECR07] the first described mutation of type B PGAM subunit that as a dimer constitutes the PGAM (EC 5.4.2.1) isoenzyme present in red blood cells. The mutation is the substitution c.690G>A (p.Met230Ile). In this report, we show that the mutated PGAM possesses an abnormal behaviour on ion-exchange chromatography and is more thermo-labile that the native enzyme. We also confirm that, similar to the PGAM isoenzymes from other sources, the BB-PGAM from human erythrocytes has a ping pong or phosphoenzyme mechanism, and that the mutation does not significantly change the K(m) and K(i) values, and the optimum pH of the enzyme. The increased instability of the mutated enzyme can account for the decreased PGAM activity in patient's red blood cells. However, the implication of a change of the k(cat) produced by the mutation cannot be discarded, since we could not determine the k(cat) value of the mutated PGAM.

Adult↗

PubMed2004

A method for estimating stochastic noise in large genetic regulatory networks.

MOTIVATION: Genetic regulatory networks are often affected by stochastic noise, due to the low number of molecules taking part in certain reactions. The networks can be simulated using stochastic techniques that model each reaction as a stochastic event. As models become increasingly large and sophisticated, however, the solution time can become excessive; particularly if one wishes to determine the effect on noise of changes to a series of parameters, or the model structure. Methods are therefore required to rapidly estimate stochastic noise. RESULTS: This paper presents an algorithm, based on error growth techniques from non-linear dynamics, to rapidly estimate the noise characteristics of genetic networks of arbitrary size. The method can also be used to determine analytical solutions for simple sub-systems. It is demonstrated on a number of cases, including a prototype model of the galactose regulatory pathway in yeast. AVAILABILITY: A software tool which incorporates the algorithm is available for use as part of the stochastic simulation package Dizzy. It is available for download at http://labs.systemsbiology.net/bolouri/software/Dizzy/ CONTACT: dorrell@systemsbiology.org SUPPLEMENTARY INFORMATION: A conceptual model of the regulatory part of the galactose utilization pathway in yeast, used as an example in the paper, is available at http://labs.systemsbiology.net/bolouri/models/galconcept.dizzy

Algorithms↗

PubMed2003

Characterization of the transit and transition times for a pathway unit of Michaelis-Menten mechanism.

The transit time and a characteristic time constant for the transition time are formulated for a pathway unit of Michaelis-Menten mechanism in metabolic chains with mass-action-type dependence. The pathway unit in a chain is assigned to each metabolite and two consecutive Michaelis-Menten-type reactions associated with it. All the relevant functions such as control coefficients, elasticities and transit time for the pathway unit are expressed in terms of the flux J and other system parameters. The transition time is characterized by a time constant for a first-order system expressed as the derivative of the total concentration of the internal metabolite with respect to the flux J.

Computer Simulation↗

PubMed2003

Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by Saccharomyces cerevisiae.

In this study we present a method for simultaneous optimization of several metabolic responses of biochemical pathways. The method, based on the use of the power law formalism to obtain a linear system in logarithmic coordinates, is applied to ethanol production by Saccharomyces cerevisiae. Starting from an experimentally based kinetic model, we translated it to its power law equivalent. With this new model representation, we then applied the multiobjective optimization method. Our intent was to maximize ethanol production and minimize each of the internal metabolite concentrations. To ensure cell viability, all optimizations were carried out under imposed constraints. The different solutions obtained, which correspond to alternative patterns of enzyme overexpression, were implemented in the original model. We discovered few discrepancies between the S-system-optimized steady state and the corresponding optimized state in the original kinetic model, thus demonstrating the suitability of the S-system representation as the basis for the optimization procedure. In all optimized solutions, the ATP level reached its maximum and any increase in its activity positively affected the optimization process. This work illustrates that in any optimization study no single criteria is of general application being the multiobjective and constrained task the proper way to address it. It is concluded that the proposed multiobjective method can serve to carry out, in a single study, the general pattern of behavior of a given metabolic system with regard to its control and optimization.

Algorithms↗

PubMed2003

Dynamic simulation of pollutant effects on the threonine pathway in Escherichia coli.

The enzymatic activities of threonine pathway in Escherichia coli are sensitive to pollutants such as cadmium, copper and mercury, which, even at low concentration, can substantially decrease or even block the pathway at several steps. Our aim was to investigate the complex effects on a metabolic pathway of such general enzyme inhibitors with several sites of action, using a previously developed computer simulation of the pathway. For this purpose, the inhibition parameters were experimentally determined and incorporated in the model. The calculation of the flux control coefficient distribution between the five steps of the threonine pathway showed that control remains shared between the three first steps under most inhibition conditions. Response coefficient analysis shows that the inhibition of aspartate semialdehyde dehydrogenase is quantitatively dominant in most circumstances.

Aspartate-Semialdehyde Dehydrogenase↗

PubMed2003

Mathematical modelling of the urea cycle. A numerical investigation into substrate channelling.

Metabolite channelling, the process in which consecutive enzymes have confined substrate transfer in metabolic pathways, has been proposed as a biochemical mechanism that has evolved because it enhances catalytic rates and protects unstable intermediates. Results from experiments on the synthesis of radioactive urea [Cheung, C., Cohen, N.S. & Raijman, L (1989) J. Biol. Chem.264, 4038-4044] have been interpreted as implying channelling of arginine between argininosuccinate lyase and arginase in permeabilized hepatocytes. To investigate this interpretation further, a mathematical model of the urea cycle was written, using Mathematica it simulates time courses of the reactions. The model includes all relevant intermediates, peripheral metabolites, and subcellular compartmentalization. Analysis of the output from the simulations supports the argument for a high degree of, but not absolute, channelling and offers insights for future experiments that could shed more light on the quantitative aspects of this phenomenon in the urea cycle and other pathways.

Arginase↗

PubMed2002

Dependence of control coefficient distribution on the boundaries of a metabolic system: a generalized analysis of the effects of additional input and output reactions to a linear pathway.

Both experimental and theoretical studies of metabolism are likely to relate to a segment that has been isolated for analytical purposes. In practice, it will be embedded in the whole of cellular metabolism. Thus, it is necessary to consider how conclusions about the control of an isolated pathway may be modified in this wider context where the input and output metabolites are considered as variables of cellular metabolism. Here, we analyse the effect of expanding a linear metabolic pathway by adding an extra input or an extra output. In particular, we analyse the effect of the elasticities of the extra steps on control coefficients. We derive matrix algebraic relationships for obtaining flux and concentration control coefficients from expressions depending on these extra elasticities and on parameters (elasticities and control coefficients) of the original pathway. These equations can be shown in certain cases to be generalized versions of earlier rescaling relationships and to be related to top-down analysis, but also apply where the new variable metabolite of the expanded pathway is an effector of more than one step of the original pathway. We use our relationships to analyse the dependence or independence of control coefficients upon these extra elasticities for the published analyses of the pathway of mammalian serine biosynthesis (Fell & Snell, 1988) and Escherischia coli threonine biosynthesis (Chassagnole et al., 2001). The same analysis can be applied to determine whether the transport reactions of substrates and products of a pathway in and out of a cell need to be included in estimations of the control coefficients of the enzymes.

Animals↗

PubMed2002

Metabolic control analysis aimed at the ribose synthesis pathways of tumor cells: a new strategy for antitumor drug development.

Metabolic control analysis predicts that effects on tumor growth are likely to be obtained with lower concentrations of drug, if an enzyme with a high control coefficient on tumor growth is being inhibited. Here we measure glucose-6-phosphate dehydrogenase (G6PDH) control coefficient on in vivo tumor growth using mice bearing Ehrlich ascites tumor cells. We used dehydroepiandrosterone-sulphate (DHEA-S), an uncompetitive inhibitor of this enzyme and the in situ cytochemical method to measure the enzyme activity changes that accompany changes on tumor cell growth. This method ensures that the enzyme activity determined is the one existing in the in situ conditions and enables computing a control coefficient in in situ conditions. From the data obtained on tumor cell number and the in situ enzyme activities in absence and presence of DHEA-S, a control coefficient of 0.41 for G6PDH on tumor cell growth was computed. This value is approximately the half of the transketolase control coefficient value of 0.9 previously reported. Moreover, the use of in situ methods to assess enzyme activities, applied for first time for the calculation of control coefficients in this study, opens new avenues to the use of uncompetitive inhibitors for the measurement of in situ control coefficients.

Animals↗

PubMed2002

Metabolic control analysis in drug discovery and disease.

Metabolic control analysis (MCA) provides a quantitative description of substrate flux in response to changes in system parameters of complex enzyme systems. Medical applications of the approach include the following: understanding the threshold effect in the manifestation of metabolic diseases; investigating the gene dose effect of aneuploidy in inducing phenotypic transformation in cancer; correlating the contributions of individual genes and phenotypic characteristics in metabolic disease (e.g., diabetes); identifying candidate enzymes in pathways suitable as targets for cancer therapy; and elucidating the function of "silent" genes by identifying metabolic features shared with genes of known pathways. MCA complements current studies of genomics and proteomics, providing a link between biochemistry and functional genomics that relates the expression of genes and gene products to cellular biochemical and physiological events. Thus, it is an important tool for the study of genotype-phenotype correlations. It allows genes to be ranked according to their importance in controlling and regulating cellular metabolic networks. We can expect that MCA will have an increasing impact on the choice of targets for intervention in drug discovery.

Aneuploidy↗