Albert Sorribas

Grx5 glutaredoxin plays a central role in protection against protein oxidative damage in Saccharomyces cerevisiae

ABSTRACT Glutaredoxins are members of a superfamily of thiol disulfide oxidoreductases involved in maintaining the redox state of target proteins. In Saccharomyces cerevisiae, two glutaredoxins (Grx1 and Grx2) containing a cysteine pair at the active site had been characterized as protecting yeast cells against oxidative damage. In this work, another subfamily of yeast glutaredoxins (Grx3, Grx4, and Grx5) that differs from the first in containing a single cysteine residue at the putative active site is described. This trait is also characteristic for a number of glutaredoxins from bacteria to humans, with which the Grx3/4/5 group has extensive homology over two regions. Mutants lacking Grx5 are partially deficient in growth in rich and minimal media and also highly sensitive to oxidative damage caused by menadione and hydrogen peroxide. A significant increase in total protein carbonyl content is constitutively observed in grx5cells, and a number of specific proteins, including transketolase, appear to be highly oxidized in this mutant. The synthetic lethality of the grx5 and grx2 mutations on one hand and ofgrx5 with the grx3 grx4 combination on the other points to a complex functional relationship among yeast glutaredoxins, with Grx5 playing a specially important role in protection against oxidative stress both during ordinary growth conditions and after externally induced damage. Grx5-deficient mutants are also sensitive to osmotic stress, which indicates a relationship between the two types of stress in yeast cells.

Mathematical models of purine metabolism in man

Experimental and clinical data on purine metabolism are collated and analyzed with three mathematical models. The first model is the result of an attempt to construct a traditional kinetic model based on Michaelis-Menten rate laws. This attempt is only partially successful, since kinetic information, while extensive, is not complete, and since qualitative information is difficult to incorporate into this type of model. The data gaps necessitate the complementation of the Michaelis-Menten model with other functional forms that can incorporate different types of data. The most convenient and established representations for this purpose are rate laws formulated as power-law functions, and these are used to construct a Complemented Michaelis-Menten (CMM) model. The other two models are pure power-law-representations, one in the form of a Generalized Mass Action (GMA) system, and the other one in the form of an S-system. The first part of the paper contains a compendium of experimental data necessary for any model of purine metabolism. This is followed by the formulation of the three models and a comparative analysis. For physiological and moderately pathological perturbations in metabolites or enzymes, the results of the three models are very similar and consistent with clinical findings. This is an encouraging result since the three models have different structures and data requirements and are based on different mathematical assumptions. Significant enzyme deficiencies are not so well modeled by the S-system model. The CMM model captures the dynamics better, but judging by comparisons with clinical observations, the best model in this case is the GMA model. The model results are discussed in some detail, along with advantages and disadvantages of each modeling strategy.

Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature.

Mathematical tools that involve the determination of systemic responses to small changes in metabolites or enzymes have demonstrated their utility for analyzing metabolic pathways. The different methodologies based on these ideas allow for modeling and analyzing biochemical pathways focusing on the coordinate behavior of the whole system. However, one must become familiar with the difference in nomenclature and methodology to relate the models and results obtained by applying these techniques and to appreciate their potential for answering fundamental questions about biochemical systems. In the following three papers we show how this can be facilitated by comparing the nomenclature, methodology, and results of the two leading techniques in this area, metabolic control analysis and biochemical systems theory, using a model of the fermentation pathway in Saccharomyces cerevisiae as a reference system. In the present paper we review the nomenclature, technical concepts, and related experimental measurements while creating a practical dictionary for the reference system that makes the relatedness of the two approaches more apparent. In the second paper, subtitled Steady-State Analysis, we show that both approaches give the same picture for many systemic responses of the reference system. In the third paper of this series, subtitled Model Validation and Dynamic Behavior, we show that the quality of the model can be assessed by studying the sensitivity to changes in the system parameters. We hope to illustrate the usefulness of these tools in providing an interpretation of the experimental measurements in a specific metabolic pathway.

Saccharomyces cerevisiae as a Model Organism: A Comparative Study

Background Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. Methodology/Principal Findings In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. Conclusions/Significance The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

A comparison of variant theories of intact biochemical systems. I. Enzyme-enzyme interactions and biochemical systems theory.

The need for a well-structured theory of intact biochemical systems becomes increasingly evident as one attempts to integrate the vast knowledge of individual molecular constituents, which has been expanding for several decades. In recent years, several apparently different approaches to the development of such a theory have been proposed. Unfortunately, the resulting theories have not been distinguished from each other, and this has led to considerable confusion with numerous duplications and rediscoveries. Detailed comparisons and critical tests of alternative theories are badly needed to reverse these unfortunate developments. In this paper we (1) characterize a specific system involving enzyme-enzyme interactions for reference in comparing alternative theories, and (2) analyze the reference system by applying the explicit S-system variant within biochemical systems theory (BST), which represents a fundamental framework based upon the power-law formalism and includes several variants. The results provide the first complete and rigorous numerical analysis within the power-law formalism of a specific biochemical system and further evidence for the accuracy of the explicit S-system variant within BST. This theory is shown to represent enzyme-enzyme interactions in a systematically structured fashion that facilitates analysis of complex biochemical systems in which these interactions play a prominent role. This representation also captures the essential character of the underlying nonlinear processes over a wide range of variation (on average 20-fold) in the independent variables of the system. In the companion paper in this issue the same reference system is analyzed by other variants within BST as well as by two additional theories within the same power-law formalism--flux-oriented and metabolic control theories. The results show how all these theories are related to one another.

Constraints Among Molecular and Systemic Properties: Implications for Physiological Genetics

Physiological genetics attempts to relate the molecular genetic properties of an organism--the genotype--to its integrated or physiological behavior--the phenotype. There has been relatively little progress in this field when compared to the neighboring fields of molecular and population genetics. This is due in part to the large number of highly non-linear interactions that characterize such systems. Biochemical Systems Theory is one approach that shows promise in dealing with the large number of non-linear interactions in a systematically structured manner. A variant of this approach has stressed the use of specific mathematical constraints, called summation and connectivity relationships, among molecular and systemic properties. In particular, the summation relationship has been used to argue that the predominance of recessive mutations is the inevitable consequence of the kinetic structure of enzyme networks and need not be attributed to natural selection. In order to put in broader perspective the implications of such constraints for physiological genetics, we have presented in this paper the outlines of the larger theory and the set of generalized steady state constraints that follow from first principles within this theory. The results show that the summation relationship suffers from a number of fundamental limitations that make it invalid for analyzing realistic biological systems. It also is shown that the more general constraint relationships, while valid, provide nothing new that cannot be obtained directly from the explicit solutions that are available within the larger theory. Thus, one can conclude that approaches based directly on the underlying equations of the system are superior to those based upon constraint relationships as a foundation for the development of physiological genetics.

Calcitonin gene-related peptide in rat spinal cord motoneurons: Subcellular distribution and changes induced by axotomy

Using light and electron microscopy, a study has been made of the changes of calcitonin gene-related peptide-like immunoreactivity in rat lumbar spinal cord motoneurons during cell body response to sciatic nerve injury. At light microscopy level, calcitonin gene-related peptide-like immunoreactivity was evaluated using an indirect immunofluorescence technique combined with Fast Blue retrograde tracing and a peroxidase-antiperoxidase procedure. The calcitonin gene-related peptide changes to sciatic nerve transection and crushing were compared. Calcitonin gene-related peptide-like immunoreactivity was transiently increased after the peripheral nerve lesion, but the response was sustained for a longer period when the peripheral nerve was transected and nerve regeneration prevented. The first changes in calcitonin gene-related peptide-like immunoreactivity were detected four days after nerve crush or transection. In animal spinal cords to which nerve crush had been applied, the maximal enhancement of immunoreactivity was found 11 days after lesion. This was followed by a gradual decline, normal levels being attained 45 days after nerve crushing. When the nerve was transected, the response was similar, but the maximal calcitonin gene-related peptide-like immunoreactivity was maintained over a period of between 11 and 30 days. As with crushing, an important decrease was observed after 45 days. The ultrastructural compartmentation of calcitonin gene-related peptide-like immunoreactivity was studied using either peroxidase-antiperoxidase method or immunogold labelling. Calcitonin gene-related peptide-like immuno-reactivity was located in restricted sacs of the Golgi complex, multivesicular bodies, small vesicles and tubulo-vesicular structures. Large, strongly labelled vesicles resembling secretory granules were also observed in neuronal bodies. Our results reveal that the increase of calcitonin gene-related peptide in motoneurons is a relevant change the cell body undergoes in response to peripheral injury. The ultrastructural location of the peptide distribution suggests specific compartmentation on tubulo-vesicular structures connected with the Golgi complex which form a network in the neuronal cytoplasm. The distribution pattern observed may be related to the sorting and delivery of calcitonin gene-related peptide to secretory vesicles.

Regulation of Motoneuronal Calcitonin Gene–related Peptide (CGRP) During Axonal Growth and Neuromuscular Synaptic Plasticity Induced by Botulinum Toxin in Rats

The aim of this study was to examine whether changes in rat motoneuronal calcitonin gene–related peptide (CGRP) can be correlated with axonal growth and plasticity of neuromuscular synapses. Nerve terminal outgrowth was induced by local paralysis with botulinum toxin. Normal adult soleus and tibialis anterior did not show detectable CGRP content at the motor endplates. Following botulinum toxin injection there was a progressive, transient and bimodal increase in CGRP in both motoneuron cell bodies which innervated poisoned muscles and their motor endplates. CGRP content was moderately increased 1 day after paralysis and, after an initial decline, reached a peak 20 days after injection. This was followed by a gradual decrease and a return to normal levels at the 200th day. CGRP changes in intoxicated endplates were less evident in the tibialis anterior than in the soleus muscle. The CGRP content in motoneurons was positively correlated with the degree of intramuscular nerve sprouting found by silver staining. In situ hybridization revealed an increase in CGRP mRNA in spinal cord motoneurons 20 days after toxin administration. We conclude that motoneurons regulate their CGRP in situations in which peripheral synapse remodelling and plasticity occur.

A comparison of variant theories of intact biochemical systems. II: Flux-oriented and metabolic control theories

In the past two decades, several theories, all ultimately based upon the same power-law formalism, have been proposed to relate the behavior of intact biochemical systems to the properties of their underlying determinants. Confusion concerning the relatedness of these alternatives has become acute because the implications of these theories have never been compared. In the preceding paper we characterized a specific system involving enzyme-enzyme interactions for reference in comparing alternative theories. We also analyzed the reference system by using an explicit variant that involves the S-system representation within biochemical systems theory (BST). We now analyze the same reference system according to two other variants within BST. First, we carry out the analysis by using an explicit variant that involves the generalized mass action representation, which includes the flux-oriented theory of Crabtree and Newsholme as a special case. Second, we carry out the analysis by using an implicit variant that involves the generalized mass action representation, which includes the metabolic control theory of Kacser and his colleagues as a special case. The explicit variants are found to provide a more complete characterization of the reference system than the implicit variants. Within each of these variant classes, the S-system representation is shown to be more mathematically tractable and accurate than the generalized mass action representation. The results allow one to make clear distinctions among the variant theories.

Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: Model validation and dynamic behavior☆

In the first two papers of this series (immediately preceding, this issue), we characterized the steady-state properties of a model of a fermentation pathway in Saccharomyces cerevisiae in four experimental conditions. In each of these conditions, the pictures obtained by metabolic control analysis and biochemical systems theory were coincident, which illustrates the relatedness of the two approaches. In this paper we analyze the quality of this description by means of the tools available within biochemical systems theory, and we show that in some of the experimental conditions studied the system is poorly characterized. The most critical condition corresponds to the immobilization of the cells at pH 5.5, in which the kinetic characterization appears to be inaccurate. Furthermore, sensitivity analysis and the study of the local steady-state stability identify the most critical parameters. The results of these analyses are confirmed by the predictions of the dynamic response of the model using its S-system representation. This illustrates the utility of these tools and warns against using the steady-state characterization without testing its validity.