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The relative contribution of mutation and selection to the amino acid substitution rates observed in empirical matrices is unclear. Herein, we present a neutral continuous fitness-stability model, inspired by the Arrhenius law (qij=aije−ΔΔGij). The model postulates that the rate of amino acid substitution (i→j) is determined by the product of a pre-exponential factor, which is influenced by the genetic code structure, and an exponential term reflecting the relative fitness of the amino acid substitutions. To assess the validity of our model, we computed changes in stability of 14,094 proteins, for which 137,073,638 in silico mutants were analyzed. These site-specific data were summarized into a 20 square matrix, whose entries, ΔΔGij, were obtained after averaging through all the sites in all the proteins. We found a significant positive correlation between these energy values and the disease-causing potential of each substitution, suggesting that the exponential term accurately summarizes the fitness effect. A remarkable observation was that amino acids that were highly destabilizing when acting as the source, tended to have little effect when acting as the destination, and vice versa (source → destination). The Arrhenius model accurately reproduced the pattern of substitution rates collected in the empirical matrices, suggesting a relevant role for the genetic code structure and a tuning role for purifying selection exerted via protein stability.

SUMMARYThe enzyme glutamine synthetase (EC 6.3.1.2) is mainly responsible for the incorporation of inorganic nitrogen into organic molecules in plants. In the present work, a new pineGS1(PpGS1b.2) gene was identified, showing a high sequence identity with theGS1b.1gene previously characterized in conifers. Phylogenetic analysis revealed that the presence ofPpGS1b.2is restricted to the generaPinusandPiceaand is not found in other conifers. Gene expression data suggest a putative role ofPpGS1b.2in plant development, similar to otherGS1bgenes from angiosperms, suggesting evolutionary convergence. The characterization of GS1b.1 and GS1b.2 at the structural, physicochemical, and kinetic levels has shown differences even though they have high sequence homology. Alterations in the kinetic characteristics produced by the site-directed mutagenesis approach carried out in this work strongly suggest an implication of amino acids at positions 264 and 267 in the active center of pine GS1b.1 and GS1b.2. Therefore, the amino acid differences between GS1b.1 and GS1b.2 would support the functioning of both enzymes to meet distinct plant needs.

Background Complex enzymatic models are required for analyzing kinetic data derived under conditions that may not satisfy the assumptions associated with Michaelis–Menten kinetics. To analyze these data, several software packages have been developed. However, the complexity introduced by these programs is often dispensable when analyzing data conforming to the canonical Michaelis–Menten model. In these cases, the sophisticated routines of these packages become inefficient and unnecessarily intricated for the intended purpose, reason for which most users resort to general-purpose graphing programs. However, this approach, in addition of being time-consuming, is prone to human error, and can lead to misleading estimates of kinetic parameters, particularly when unweighted regression analyses of transformed kinetic data are performed. Results To fill the existing gap between highly specialized and general-purpose software, we have developed an easy-to-use R package, renz, designed for accurate and efficient estimation of enzyme kinetic parameters. The package provides different methods that can be clustered into four categories, depending on whether they are based on data fitting to a single progress curve (evolution of substrate concentration over time) or, alternatively, based on the dependency of initial rates on substrate concentration (differential rate equation). A second criterion to be considered is whether the experimental data need to be manipulated to obtain linear functions or, alternatively, data are directly fitted using non-linear regression analysis. The current program is a cross-platform, free and open-source software that can be obtained from the CRAN repository. The package is accompanied by five vignettes, which are intended to guide users to choose the appropriate method in each case, as well as providing the basic theoretical foundations of each method. These vignettes use real experimental data to illustrate the use of the package utilities. Conclusions renz is a rigorous and yet easy-to-use software devoted to the analysis of kinetic data. This application has been designed to meet the needs of users who are not practicing enzymologists, but who need to accurately estimate the kinetic parameters of enzymes. The current software saves time and minimizes the risk of making mistakes or introducing biases due to uncorrected error propagation effects.

Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.

Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.

Methionine in proteins, apart from its role in the initiation of translation, is assumed to play a simple structural role in the hydrophobic core, in a similar way to other hydrophobic amino acids such as leucine, isoleucine, and valine. However, research from a number of laboratories supports the concept that methionine serves as an important cellular antioxidant, stabilizes the structure of proteins, participates in the sequence-independent recognition of protein surfaces, and can act as a regulatory switch through reversible oxidation and reduction. Despite all these evidences, the role of methionine in protein structure and function is largely overlooked by most biochemists. Thus, the main aim of the current article is not so much to carry out an exhaustive review of the many and diverse processes in which methionine residues are involved, but to review some illustrative examples that may help the nonspecialized reader to form a richer and more precise insight regarding the role-played by methionine residues in such processes.

We are living in the Big Data era, and yet we may have serious troubles when dealing with a handful of kinetic data if we are not properly instructed. The aim of this paper, related to enzyme kinetics, is to illustrate how to determine the Km and Vmax of a michaelian enzyme avoiding the pitfalls in which we often fall. To this end, we will resort to kinetic data obtained by second-year Biochemistry students during a laboratory experiment using β-galactosidase as an enzyme model, assayed at different concentrations of its substrate. When these data were analyzed using conventional linear regression of double-reciprocal plots, the range of Km and Vmax values obtained by different students varied widely. Even worse, some students obtained negative values for the kinetic parameters. Although such a scenario could make us think of a wide inter-student variability regarding their skills to obtain reliable data, the reality was quite different: when properly analyzed (accounting for error propagation) the data obtained by all the students were good enough to allow a correct estimation of the Km (2.8 ± 0.3 mM) and Vmax (179 ± 27 mM/min) with a reduced intergroup standard deviation. A student-accessible discussion of the importance of weighted linear regression in biochemical sciences is provided.

Methionine-rich prion-like proteins can regulate liquid–liquid phase separation processes in response to stresses. To date, however, very few proteins have been identified as methionine-rich prion-like. Herein, we have performed a computational survey of the human proteome to search for methionine-rich prion-like domains. We present a census of 51 manually curated methionine-rich prion-like proteins. Our results show that these proteins tend to be modular in nature, with molecular sizes significantly greater than those we would expect due to random sampling effects. These proteins also exhibit a remarkably high degree of spatial compaction when compared to average human proteins, even when protein size is accounted for. Computational evidence suggests that such a high degree of compactness might be due to the aggregation of methionine residues, pointing to a potential redox regulation of compactness. Gene ontology and network analyses, performed to shed light on the biological processes in which these proteins might participate, indicate that methionine-rich and non-methionine-rich prion-like proteins share gene ontology terms related to the regulation of transcription and translation but, more interestingly, these analyses also reveal that proteins from the methionine-rich group tend to share more gene ontology terms among them than they do with their non-methionine-rich prion-like counterparts.

The ability to make decisions at the cellular level is absolutely critical for the survival of organisms. Eukaryotic cells are constantly making binary decisions in response to internal and environmental signals. Among the most notable transducers of information are protein kinases. The regulation of these signaling proteins often relies on the activity of other protein kinases located upstream in the signaling cascade. However, these signaling systems are by their own nature an important source of molecular noise. Herein, we have assessed the role of multisite phosphorylation in detecting signals in the face of molecular noise. To address this issue, we have conceptually envisioned the biochemical transduction machinery as a classifier model that can lead to four possible outputs: true positives and negatives, and false positives and negatives. In this probabilistic framework, we show that multisite phosphorylation represents a mechanism to filter noise during the decision-making process. We present results showing that nonessential phosphorylation sites contribute to increase the rate of true positives while, at the same time, they can lessen the rate of false positives. This simultaneous increase in sensitivity and specificity, makes multisite phosphorylation a valuable and easily implemented mechanism to reliably transduce information in noisy contexts.

Methionine is a proteinogenic amino acid that can be post-translationally modified. It is now well established that reactive oxygen species can oxidise methionine residues within living cells. For a long time, it has been thought that such a modification represents merely an inevitable damage derived from aerobic metabolism. However, several authors have begun to contemplate a possible role for this methionine modification in cell signalling. During the last years, a number of proteomic studies have been carried out with the purpose of detecting proteins containing oxidised methionines. Although these proteomic works allow to pinpoint those methionines being oxidised, they are also arduous, expensive and time-consuming. For these reasons, computational approaches aimed at predicting methionine oxidation sites in proteins become an appealing alternative. In the current work, we address methionine oxidation prediction by combining computational intelligence methods with feature engineering and feature selection techniques to improve the efficacy of several machine learning models, while reducing the number of input characteristics needed to get high accuracy rates. We compare random forests, support vector machines, neural networks and flexible discriminant analysis models. Random forests give the best AUC ($$0.8124 \pm 0.0334$$) and accuracy rates ($$0.7590 \pm 0.0551$$) by using only a reduced set of 16 characteristics. These results surpass the outcomes of previous works. In addition, we present an end-user script that has been developed to take a protein ID as an input and return a list with the oxidation state of all the methionine residues found in the analysed protein. Finally, to illustrate the applicability of this tool, we have selected the human $$\alpha 1$$-antitrypsin protein as a case study. This protein was selected because it was not present among the set of proteins used to build up the predictive models but the protein has been well characterised experimentally in terms of methionine oxidation. The prediction returned by our script fully matches the empirical evidence. Out of the nine methionine residues found in this protein, our model predicts the oxidation of only two of them, M351 and M358, which have been reported, on the base of mass spectrometry analyses, to be particularly susceptible to oxidation.

Summary Methionine sulfoxidation is a posttranslational modification (PTM) playing important roles in cell signaling. Herein, we present ptm, an R package for the study of this modification. However, since many of the analyses applied to methionine modification can be extended to other modifications, the package can be useful to thoroughly analyze PTMs in general. Thus, within a single software environment, ptm can integrate information from up to 11 databases covering nine modifications. Different functions can work coordinately to form pipelines allowing the programmatic analysis of thousands of proteins. Alternatively, the user can simultaneously perform different analyses on the same protein of interest, combining the results into a single output. The flexibility of ptm makes it a suitable tool to address site- and protein-centric hypotheses related to PTMs. Accompanying the package, we maintain a web page containing extended documentation and examples of the tasks that can be performed with ptm. Availability and implementation ptm is implemented in R. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://bitbucket.org/jcaledo/ptm. Extended documentation can be found at https://metositeptm.com Supplementary information Supplementary data are available at Bioinformatics online.

Thermodynamics arose with an eminent practical vocation. Through time, it has evolved into a theory that has found utility in many scientific fields. However, the way to approach the study and the sort of insights we pursue varies from one discipline to another, even when the thermodynamic fundamentals are the same. Herein, we will pay attention to both facets: the universal principle of thermodynamics, and the particular features of biochemical systems. First, we will introduce basic concepts from both classical and nonequilibrium thermodynamics. Subsequently, we will point out those particular aspects that should be considered when a chemical reaction is taking place within the system. Afterward, the enzyme-mediated catalysis will be presented from a thermodynamic point of view. Finally, we will show some concrete examples that illustrate how the use of thermodynamic elements allows a better and deeper understanding of the structure, performance, and evolution of metabolic pathways.

Although reactive oxygen species are best known as damaging agents linked to aerobic metabolism, it is now clear that they can also function as messengers in cellular signalling processes. Methionine, one of the two sulphur containing amino acids in proteins, is liable to be oxidized by a well-known reactive oxygen species: hydrogen peroxide. The awareness that methionine oxidation may provide a mechanism to the modulation of a wide range of protein functions and cellular processes has recently encouraged proteomic approaches. However, these experimental studies are considerably time-consuming, labor-intensive and expensive, thus making the development of in silico methods for predicting methionine oxidation sites highly desirable. In the field of protein phosphorylation, computational prediction of phosphorylation sites has emerged as a popular alternative approach. On the other hand, very few in-silico studies for methionine oxidation prediction exist in the literature. In the current study we have addressed this issue by developing predictive models based on machine learning strategies and models—random forests, support vector machines, neural networks and flexible discriminant analysis—, aimed at accurate prediction of methionine oxidation sites.

In yeast, a sudden transition from glucose limitation to glucose excess leads to a new steady state at increased metabolic fluxes with a sustained decrease in the ATP concentration. Although this behaviour has been rationalized as an adaptive metabolic strategy, the mechanism behind it remains unclear. Nevertheless, it is thought that, on glucose addition, a metabolite derived from glycolysis may up-regulate ATP-consuming reactions. The adenine nucleotides themselves have been ruled out as the signals that mediate this regulation. This is mainly because, in that case, it would be expected that the new steady state at increased fluxes would be accompanied by an increased stationary ATP concentration. In this study, we present a core model consisting of a monocyclic interconvertible enzyme system. Using a supply–demand approach, we demonstrate that this system can account for the empirical observations without involving metabolites other than the adenine nucleotides as effectors. Moreover, memory is an emerging property of such a system, which may allow the cell to sense both the current energy status and the direction of the changes.

This paper addresses some questions related to the evolution of cooperative behaviors, in the context of energetic metabolism. Glycolysis can perform either under a dissipative working regime suitable for rapid proliferation or under an efficient regime that entails a good modus operandi under conditions of glucose shortage. A cellular mechanism allowing switching between these two regimes may represent an evolutionary achievement. Thus, we have explored the conditions that might have favored the emergence of such an accommodative mechanism. Because of an inevitable conflict for resources between individual interests and the common good, rapid and inefficient use of glucose is always favored by natural selection in spatially homogeneous environment, regardless of the external conditions. In contrast, when the space is structured, the behavior of the system is determined by its free energy content. If the fuel is abundant, the dissipative strategy dominates the space. However, under famine conditions the efficient regime represents an evolutionary stable strategy in a Harmony game. Between these two extreme situations, both metabolic regimes are engaged in a Prisoner's Dilemma game, where the output depends on the extracellular free energy. The energy transition values that lead from one domain to another have been calculated. We conclude that an accommodative mechanism permitting alternation between dissipative and efficient regimes might have evolved in heterogeneous and highly fluctuating environments. Overall, the current work shows how evolutionary optimization and game-theoretical approaches can be complementary in providing useful insights into biochemical systems.

In contraposition to the view of aging as a stochastic time-dependent accumulation of damage, phenoptotic theories of aging postulate that senescence may provide supra-individual advantages, and therefore it might have been promoted by natural selection. We reason that although programmed aging theories are subjectively appealing because they convey a cure for aging, they also raise a number of objections that need to be dealt with, before we may be entitled to contemplate aging as an adaptive function evolved through natural selection. As an alternative view, we present metabolism as an endless source of by-products and errors causing cellular damage. Although this damage accumulation event is a spontaneous entropy-driven process, its kinetics can be genetically and environmentally modulated, giving place to the wide range of lifespans we observe. Mild forms of damage may be accumulating during a long enough period of time to allow reproduction before the fatal failure happens. Hence, aging would be a stochastic process out of the reach of natural selection. However, those genetic pathways influencing the rate of aging and consequently determining longevity may be targets of natural selection and may contribute to shaping the optimal strategy according to the ecological context. In this sense, short- and long-lived organisms represent two extreme strategies that, in terms of biological fitness, can perform equally well, each within its own niche.

When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature coefficients (Q10, defined as the rate change that parallels a 10 °C temperature shift) can be expected. We show why this approach, which is appropriate under saturation conditions, is unsuitable for those enzymes working at subsaturating concentrations of their substrates. To overcome this limitation, we present and discuss a simple thermokinetic treatment of the Michaelis−Menten model for the enzyme-catalyzed reaction.

Phosphate-activated glutaminase has a critical role in tumours and rapidly dividing cells and its activity is correlated with malignancy. Ehrlich ascites tumour cells transfected with the pcDNA3 vector containing an antisense segment (0.28 kb) of rat kidney glutaminase showed impairment in the growth rate and plating efficiency, as well as a shortage in the glutaminase protein and activity. The C-terminal segment used is well conserved in all glutaminase sequences known. The transfected cells, named 0.28AS-2, displayed remarkable changes in their morphology compared with the parental cell line. The 0.28AS-2 cells also lost their tumourigenic capacity in vivo. Control mice developed an ascitic tumour, with a lifespan of 16±1 days, when inoculated with 107 cells/mouse; on the contrary, animals inoculated with transfected cells up to 2.5 times the cell numbers of control mice did not develop tumours and behaved as healthy animals. The ability to revert the transformed phenotype of antisense-transfected cells confirms the relevance of glutaminase in the transformation process and could provide new ways for the study of gene therapy.

Phosphate-activated glutaminase (GA) is overexpressed in certain types of tumour but its exact role in tumour cell growth and proliferation is unknown. Here we describe the isolation of a full-length cDNA clone of human breast cancer ZR75 cells, by a combination of λgt10 cDNA library screening and the rapid amplification of cDNA ends (‘RACE’) technique. The cDNA of human GA is 2408 nt with a 1806-base open reading frame encoding a 602-residue protein with a predicted molecular mass of 66309 Da. The deduced amino acid sequence contains a putative mitochondrial import presequence of 14 residues at the N-terminal end. Heterologous expression and purification in Escherichia coli yielded a product of the expected molecular size that was recognized by using antibodies against the recombinant human GA. Sequence analyses showed that human GA was highly similar to the rat liver enzyme. Northern gel analysis revealed that the gene is present in human liver, brain and pancreas, in which a major transcript of 2.4 kb was demonstrated, but not in kidney, heart, skeletal muscle, lung or placenta. These results strongly suggest that the first human GA cloned, the GA from ZR-75 breast cancer cells, and presumably those from human liver and brain, are liver-type isoenzymes, in sharp contrast with the present view that considers the kidney type as the isoform expressed in all tissues with GA activity, with the exception of postnatal liver.

The pH dependence of the phosphate-activated glutaminase isolated from Ehrlich tumour cells suggests a functional role for two prototropic groups with apparent pKa of 9.3 and 7.7 at the active site of the protein; these pKa values are compatible with cysteine and histidine residues, respectively. This possibility was investigated by chemical modification studies of the purified enzyme. N-Ethylmaleimide fully inactivated the purified glutaminase; the reaction order was very close to 1.0, suggesting that N-ethylmaleimide modifies glutaminase at a single essential site. Spectrophotometric studies of the isolated protein treated with diethyl pyrocarbonate indicate that two histidine residues are modified. Since glutaminase is loosely associated to the inner mitochondrial membrane, modification experiments were also carried out using mitochondrial membrane fractions. N-Ethylmaleimide and diethyl pyrocarbonate gave similar results in mitochondria membrane-bound enzyme to those obtained with purified enzyme. Glutamate, which behaves as a competitive inhibitor of the enzyme, partially protected the inactivation caused by N-ethylmaleimide in membrane-bound experiments. The results suggest the existence of a critical histidine residue(s) in the tumour glutaminase, and strongly support the notion that a cysteine residue, which is located at (or near) the active site, is involved in the catalytic mechanism as well.

Acute insulin stimulation of glucose transport in fat and skeletal muscle occurs principally as a result of the hormonal induced translocation of the GLUT4 glucose transporter from intracellular vesicular stores to the plasma membrane. The precise mechanisms governing the fusion of GLUT4 vesicles with the plasma membrane are very poorly understood at present but may share some similarities with synaptic vesicle fusion, as vesicle-associated membrane protein (VAMP) and cellubrevin, two proteins implicated in the process of membrane fusion, are resident in GLUT4-containing vesicles isolated from rat and murine 3T3-L1 adipocytes respectively. In this study we show that proteolysis of both cellubrevin and VAMP, induced by electroporation of isolated rat adipocytes with tetanus toxin, does not impair insulin-stimulated glucose transport or GLUT4 translocation. The hormone was found to stimulate glucose uptake by approx. 16-fold in freshly isolated rat adipocytes. After a single electroporating pulse, the ability of insulin to activate glucose uptake was lowered, but the observed stimulation was nevertheless nearly 5-fold higher than the basal rate of glucose uptake. Electroporation of adipocytes with 600 nM tetanus toxin resulted in a complete loss of both cellubrevin and VAMP expression within 60 min. However, toxin-mediated proteolysis of both these proteins had no effect on the ability of insulin to stimulate glucose transport which was elevated approx. 5-fold, an activation of comparable magnitude to that observed in cells electroporated without tetanus toxin. The lack of any significant change in insulin-stimulated glucose transport was consistent with the finding that toxin-mediated proteolysis of both cellubrevin and VAMP had no detectable effect on insulin-induced translocation of GLUT4 in adipocytes. Our findings indicate that, although cellubrevin and VAMP are resident proteins in adipocyte GLUT4-containing vesicles, they are not required for the acute insulin-induced delivery of GLUT4 to the plasma membrane.

Mitochondrial-inner-membrane vesicles, isolated from Ehrlich ascites carcinoma cells by titration with detergents, accumulated L-glutamine by a very efficient transport system. The vesicles lack any phosphate-activated glutaminase activity, allowing measurement of transport rates without interference by L-glutamine metabolism. The time course of the transport was linear for the first 60 s, reaching a steady state after 120 min. L-Glutamine transport showed co-operativity, with a Hill coefficient of 2.2; the kinetic parameters S0.5 and Vmax had values of 5 mM and 26 nmol/30 s per mg of protein respectively. The pH-dependence curve showed a bell shape, with a pH optimum about 8.0. The uptake of L-glutamine was not affected by the presence of a 50-fold molar excess of D-glutamine, L-cysteine, L-histidine, L-alanine, L-serine and L-leucine, whereas L-glutamate behaved as a poor inhibitor. The structural analogue L-glutamate gamma-hydroxamate (5mM) inhibited the net uptake by 68%; interestingly, other analogues (6-diazo-5-oxo-L-norleucine, acivicin and L-glutamate gamma-hydrazide) were ineffective. The impermeant thiol reagent p-chloromercuriphenylsulphonic acid (0.5mM) completely abolished the mitochondrial L-glutamine uptake; in contrast, other thiol reagents (mersalyl and N-ethylmaleimide) did not significantly affect the transport. These data confirm the existence of a specific transport system with high capacity for L-glutamine in the mitochondrial inner membrane, a step preceding the highly operative glutaminolysis in tumour cells.

Two alternative purification schemes to obtain the glutaminase from Ehrlich tumor cells in a highly purified form have been developed. One experimental approach is based on conventional and high-performance liquid chromatography fractionation techniques, yielding a 37-fold higher purification than has been previously reported. The method comprises: isolation of mitochondria, solubilization with Triton X-100, ion-exchange and hydroxyapatite chromatography, ammonium sulfate precipitation, and hydrophobic interaction chromatography. A second purification schedule has been optimized employing native polyacrylamide gel electrophoresis, in situ activity staining, and electroelution of the protein band. This approach resulted in a simple and rapid isolation of a 10-fold higher purified glutaminase than before, minimizing also the potential for proteolytic inactivation of the enzyme. The apparent molecular weight of the protein in native form was determined by gel filtration and sucrose density gradient ultracentrifugation. Polyclonal antibodies raised against Ehrlich glutaminase were immunopurified against the pig kidney enzyme. Immunoblot analyses employing these antibodies as well as anti-rat kidney glutaminase antibodies revealed the same pattern of bands seen with the purified enzyme.

During the course of evolution, amino acid shifts might have resulted in mitochondrial proteomes better endowed to resist oxidative stress. However, owing to the problem of distinguishing between functional constraints/adaptations in protein sequences and mutation-driven biases in the composition of these sequences, the adaptive value of such amino acid shifts remains under discussion. We have analyzed the coding sequences of mtDNA from 173 mammalian species, dissecting the effect of nucleotide composition on amino acid usages. We found remarkable cysteine avoidance in mtDNA-encoded proteins. However, no effect of longevity on cysteine content could be detected. On the other hand, nucleotide compositional shifts fully accounted for threonine usages. In spite of a strong effect of mutational bias on methionine abundances, our results suggest a role of selection in determining the composition of methionine. Whether this selective effect is linked or not to protection against oxidative stress is still a subject of debate.

By using a combination of evolutionary and structural data from 231 species, we have addressed the relationship between evolution and structural features of cytochrome b and COX I, two mtDNA-encoded proteins. The interior of cytochrome b, in contrast to that of COX I, exhibits a remarkable tolerance to changes. The higher evolvability of cytochrome b contrasts with the lower rate of synonymous substitutions of its gene when compared to that of COX I, suggesting that the latter is subjected to a stronger purifying selection. We present evidences that the stability effect of mutations (ΔΔG) may be behind these differential behaviour.

A hallmark of living matter is its ability to extract and transform energy from the environment. Not surprisingly, biology students are required to take thermodynamics. The necessity of coupling exergonic reactions to endergonic processes is easily grasped by most undergraduate students. However, when addressing the thermodynamic concept of coupled reactions, both students and textbook authors often make claims that clash with the Second Law of Thermodynamics. Herein, I point out the most common flaws, analyze the causes leading to these mistakes, and suggest a few rules to avoid them.

Methionine residues in proteins react readily with reactive oxygen species making them particularly sensitive to oxidation. However, because oxidized methionine can be reduced back in a catalyzed reaction, it has been suggested that methionine residues act as oxidant scavengers, protecting not only the proteins where they are located but also the surrounding macromolecules. To investigate whether methionine residues may be selected for or against animal longevity, we carried out a meta-examination of mitochondrial genomes from mammalian species. Our analyses unveiled a hitherto unnoticed observation: mitochondrially encoded polypeptides from short-lived species are enriched in methionine when compared with their long-lived counterparts. We show evidence suggesting that methionine addition to proteins in short-lived species, rather than methionine loss from proteins in long-lived species, is behind the reported difference in methionine usage. The inverse association between longevity and methionine, which persisted after correction for body mass and phylogenetic interdependence, was paralleled by the methionine codon AUA, but not by the codon AUG. Although nuclear encoded mitochondrial polypeptides exhibited higher methionine usage than nonmitochondrial proteins, correlation with longevity was only found within the group of those polypeptides located in the inner mitochondrial membrane. Based on these results, we propose that short-lived animals subjected to higher oxidative stress selectively accumulate methionine in their mitochondrially encoded proteins, which supports the role of oxidative damage in aging.

Glycolysis, an ancient energy-processing pathway, can operate either under an efficient but slow regime or, alternatively, under a dissipative but fast-working regime. Trading an increase in efficiency for a decrease in rate represents a cooperative behavior, while a dissipative metabolism can be regarded as a cheating strategy. Herein, using irreversible thermodynamic principles and methods derived from game theory, we investigate whether, and under what conditions, the interplay between these two metabolic strategies may have promoted the clustering of undifferentiated cells. In the current model, multicellularity implies the loss of motility, which represents a hindrance rather than a improvement when competing with mobile single-celled organisms. Despite that, when considering glycolysis as the only energy-processing pathway, we conclude that cells endowed with a low basal anabolic metabolism may have benefited from clustering when faced to compete with cells exhibiting a high anabolic activity. The current results suggest that the transition to multicellularity may have taken place much earlier than hitherto thought, providing support for an extended period of Precambrian metazoan diversification.

Glutamatergic signalling plays an important role in the coordination of hormone secretion from the endocrine pancreas. Thus, glutamate production must be a process exquisitely regulated to ensure a proper transmitter function. Recently we have reported that the endocrine pancreas co-expresses two isoforms of the protein glutaminase (GA), denoted as kidney-type (KGA) and liver-type (LGA). However, how GA activity, and therefore glutamate production, is regulated in the islets represents a critical issue that remains unresolved. Since the purification of these enzymes from rat islets is a daunting task, in order to characterize each isoform we have taken advantage of the spatial segregation of these isoenzymes in pancreas. To assist us with this goal, we have developed a new procedure that enables us to assay GA activity in situ. The assay is highly specific for GA as indicated by its dependence on glutamine and orthophosphate. Surprisingly, LGA, which is abundantly expressed by beta-cells, did not show detectable activity under the assay conditions. All the GA activity detected in pancreatic islets was attributed to KGA and was confined to the mantle of the islets. Double labelling analyses strongly suggested that alpha-cells should be regarded as the site of glutamate production in the endocrine pancreas.

In skeletal muscle, acute insulin treatment results in the recruitment of the GLUT4 glucose transporter from intracellular vesicular structures to the plasma membrane. The precise nature of these intracellular GLUT4 stores has, however, remained poorly defined. Using an established skeletal-muscle fractionation procedure we present evidence for the existence of two distinct intracellular GLUT4 compartments. We have shown that after fractionation of crude muscle membranes on a discontinuous sucrose gradient the majority of the GLUT4 immunoreactivity was largely present in two sucrose fractions (30 and 35%, w/w, sucrose; denoted F30 and F35 respectively) containing intracellular membranes of different buoyant densities. Here we show that these fractions contained 44±6 and 49±7% of the crude membrane GLUT4 reactivity respectively, and could be further discriminated on the basis of their immunoreactivity against specific subcellular antigen markers. Membranes from the F30 fraction were highly enriched in transferrin receptor (TfR) and annexin II, two markers of the early endosome compartment, whereas they were significantly depleted of both GLUT1 and the α1-subunit of (Na++K+)-ATPase, two cell-surface markers. Insulin treatment resulted in a significant reduction in GLUT4 content in membranes from the F35 fraction, whereas the amount of GLUT4 in the less dense (F30) fraction remained unaffected by insulin. Immunoprecipitation of GLUT4-containing vesicles from both intracellular fractions revealed that TfR was present in GLUT4 vesicles isolated from membranes from the F30 fraction. In contrast, GLUT4 vesicles from the F35 fraction were devoid of TfR. The aminopeptidase, vp165, was present in GLUT4 vesicles from both F30 and F35; however, vesicles isolated from F30 contained over twice as much vp165 per unit of GLUT4 than those isolated from F35. The biochemical co-localization of vp165/GLUT4 was further substantiated by double-immunogold labelling of ultrathin muscle sections. Overall, our data indicate the presence of at least two internal GLUT4 pools: one possibly derived from an endosomal recycling compartment, and the other representing a specialized insulin-sensitive GLUT4 storage pool. Both pools contain vp165.

The intramitocondrial localization of the phosphate-activated glutaminase from Ehrlich cells has been examined by a combination of techniques, including: mitochondria subfractionation studies, chemical modification with sulfhydryl group reagents of different permeability, enzymatic digestion in both sides of the inner mitochondrial membrane, and immunological studies. Using alkaline extraction at high ionic strength, hypoosmotic shock and freezing-thawing cycle techniques, the enzyme was found in the particulate fraction. On the contrary, glutaminase activity was labile when subfractionation was carried out by digitonin/lubrol method; Western blot analysis localized the inactive enzyme in the matrix fraction. In addition, glutaminase was fully inactivated when mitoplasts were incubated with phospholipase A2 and phospholipase C. The enzyme also showed a non-linear Arrhenius plot with a break at 24 degrees C. The membrane-impermeant thiol reagents mersalyl and p-chloromercuriphenylsulfonic acid do not inhibit glutaminase activity in freeze-thawed mitochondria and mitoplasts, but N-ethylmaleimide, which is membrane permeant, strongly inhibited the enzyme. However, mersalyl and p-chloromercuriphenylsulfonic acid were effective inhibitors when the alkylation was performed on the matrix side of mitoplasts or using detergent-solubilized enzyme. Furthermore, trypsin digestion of mitoplasts was only effective inactivating glutaminase when the proteolysis was carried out on the matrix side of the vesicles. Enzyme-linked immunosorbent assay of the soluble and membrane fractions obtained in the preparation of submitochondrial particles, revealed that most of the enzyme was solubilized, but in the inactive form. Phase separation with Triton X-114 rendered most of the protein in the aqueous phase. These results taken together discard a transmembrane localization for the protein, whereas they are consistent with anchorage of glutaminase on the matrix side of the inner mitochondrial membrane, the matrix portion of the enzyme being relevant for its function.

The role of Rab4, a small molecular weight GTP binding protein implicated in endosomal/plasma membrane (PM) recycling, in the translocation of the GLUT4 transporter in rat skeletal muscle was studied. Muscle membranes, prepared by subcellular fractionation of control and insulin treated rat skeletal muscle, were subjected to SDS/PAGE and immunoblot analyses. Insulin treatment caused an increase in GLUT4 in a plasma membrane (PM) enriched fraction from an intracellular membrane (IM) fraction. Immunoprecipitation of GLUT4 vesicles from the IM compartment revealed that Rab4 could be coprecipitated. Importantly, however, and unlike in adipocytes, immunoisolated GLUT4 vesicles from rat skeletal muscle contained no detectable immunoreactivity towards the transferrin receptor, suggesting that Rab4 was present in a GLUT4 IM pool that was not characteristic of early endosomes. The involvement of Rab4 in GLUT4 translocation was further supported by the finding that insulin treatment resulted in a significant (43%) reduction in Rab4 in the IM compartment. Our results suggest (i) that insulin induces the loss of both GLUT4 and Rab4 from the same IM compartment, (ii) that Rab4 may be involved in GLUT4 translocation based on its coprecipitation with the transporter from the insulin-sensitive pool and (iii) that Rab4 can be localized to intracellular membranes which appear not to be of early endosome origin.

Changes in phosphate-activated glutaminase activities determined in intact cells and isolated mitochondria have been followed during mouse Ehrlich ascites carcinoma development. Glutaminase activities parallel the levels of poly(A)+ RNAs encoding for the mitochondrial phosphate activated glutaminase. During the exponential growth phase, maximum activity was observed and the relative abundance of glutaminase mRNA significantly increased with regard to the stationary growth phase. The presented results show that tumor phosphate-activated glutaminase is subject to long-term regulation by differential gene expression.

A new procedure for the analysis and detection of phosphate-activated glutaminase (EC 3.5.1.2) by native electrophoresis has been developed. The method is based on the in situ detection of glutaminase activity in two different systems of native polyacrylamide gradient gels, containing 3-(3-cholamidopropyl)-dimethyl-ammonio-1-propane sulfonate (CHAPS) or Triton X-100 as nondenaturant detergents. Crude Triton X-100 extracts of mitochondria were resolved by electrophoresis. The enzyme was specifically revealed by incubation of the gel with glutamine and coupling the oxidation of the glutamate formed to the reduction of a tetrazolium dye, in the presence of glutamate dehydrogenase trapped in a 1% agar solid overlay. Both Ehrlich ascitic cell and mouse kidney glutaminases were resolved by native electrophoresis and specifically detected with the activity staining. Moreover, the redox-cycling staining was tested in solution, showing linearity with the amount of glutamate or glutaminase activity present. The method described could be a useful tool for native polyacrylamide gel electrophoresis of membrane proteins.

A recent paper published in PLoS Biology [1] deals with the contention of whether the rates of morphological evolution are accelerated on islands relative to the mainland. Because of the scarcity of empirical data, the long-held supposition that insular mammals can evolve faster than their continental counterparts remains debatable. In this context, the work in [1] represents a valuable contribution. Indeed, the author has collected and provided a wealth of data of considerable interest. Nevertheless, the main conclusion of [1] may not be fully supported by the data when they are critically analysed. In the cited work, island and mainland rate comparisons were carried out by regression analyses obtained when log rates in darwins were plotted against log times in million years. The author claimed that the regression line of the island species was above the line of the mainland species over a large range of data, indicating that the evolutionary rates for island species were greater than those for mainland species. However, this claim deserves some reflection. Rates in darwins (d) were calculated as (ln x2– ln x1)/Δt, where x1 and x2 correspond to linear measurements of the same structure for a descendant and its ancestor, which are separated by Δt million years. Whenever using the darwin to describe the evolutionary rate of change, a caveat must be born in mind: darwins accurately describe rates of change, only provided that evolutionary changes (ln x2– ln x1) resulted from steady accumulation in a monotonic fashion over the entire period of time (Δt). If this is not the case, then the resulting rates of evolution may be mathematical artefacts of the length of the interval over which they are measured. In other words, the values obtained will not describe solely the sequence of changes and their tempo, but rather will include dependences on the arbitrary choices of starting and ending points from which the rates are calculated [2]. The difficulties related to the implicit assumption of a monotonic relationship between change and elapsed time, with no provision for reversal changes or punctuation, becomes especially relevant when comparing data differing widely in their time intervals. This seems to be the case in [1], where there are fewer island data points for the largest time intervals (six higher than 21,000 y) and fewer mainland data points for the smallest time intervals (two below 2,400 y). Not surprisingly, under these circumstances, data from islands showed higher values of d than their continental counterpart, despite the lack of a significant difference in their evolutionary changes. In contrast, when only those samples from island and mainland that were sampled over the same period of time (2,400–21,000 y) were included in the analysis, we failed to detect any significant difference in the rate of morphological evolution among insular and continental mammals. An accelerated evolution among island mammals may be a real feature that we do not refuse. However, the validity of this claim remains an open question that deserves further research. In any event, we should be aware of the necessity to provide reliable analyses, free of those mathematical artefacts associated with the interpretation of data.

We have investigated the effect of chronic competitive inhibition of SNAT2 (System A) amino acid (AA) transport, induced by incubation with a saturating dose of a non-metabolisable System A amino acid analogue (Me-AIB), on growth and proliferation of MCF-7 human breast cancer cells in complete culture medium. These cells express Na+- and pH-dependent SNAT2 AA transport and a saturating concentration of Me-AIB (10 mM) competitively inhibits (90%) AA uptake via SNAT2. Incubation with Me-AIB for up to 5 days progressively reduced cell proliferation (~2-fold) and depleted intracellular concentrations of not only SNAT2 AA substrates but of essential branched chain AAs (e.g. leucine). Surprisingly, total cellular protein was maintained and cells subjected to chronic Me-AIB incubation exhibited a detectable increase in cell size. Analysis of mTOR signalling revealed that, despite a substantial reduction in size of the intracellular AA pool, Me-AIB elevated mTOR-dependent p70S6K1 phosphorylation. Proteomic analysis of TAP-tag purified SNAT2 fusion proteins identified two novel SNAT2-interacting proteins that may potentially function in conjunction with the SNAT2 transceptor to regulate signalling pathways influencing protein turnover and cell growth.