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Ras proteins were highly conserved during evolution. They function as a point of convergence for different signalling pathways in eukaryotes and are involved in a wide range of cellular responses (shift from gluconeogenic to fermentative growth, breakdown of storage carbohydrates, stress resistance, growth control and determination of life span, morphogenesis and development, and others). These proteins are members of the small GTPase superfamily, which are active in the GTP-bound form and inactive in the GDP-bound form. Given the importance of studies on the Ras protein activation state to understand the detailed mechanism of Ras-mediated signal transduction, we provide here a simple, sensitive, and reliable method, based on the high affinity interaction of Ras-GTP with the Ras binding domain (RBD) of Raf1, to measure the level of Ras2-GTP on total Ras2 in Saccharomyces cerevisiae. Moreover, to study the localization of Ras-GTP in vivo in single S. Cerevisiae cells, we expressed a probe consisting of a GFP fusion with a trimeric Ras Binding Domain of Raf1 (eGFP-RBD3), which was proven to be a useful live-cell biosensor for Ras-GTP in mammalian cells. © 2014 Springer Science+Business Media, LLC.

For centuries yeast species have been popular hosts for classical biotechnology processes, such as baking, brewing, and wine making, and more recently for recombinant proteins production, thanks to the advantages of unicellular organisms (i.e., ease of genetic manipulation and rapid growth) together with the ability to perform eukaryotic posttranslational modifications. Moreover, yeast cells have been used for few decades as a tool for identifying the genes and pathways involved in basic cellular processes such as the cell cycle, aging, and stress response.In the budding yeast S. cerevisiae the Ras/cAMP/PKA pathway is directly involved in the regulation of metabolism, cell growth, stress resistance, and proliferation in response to the availability of nutrients and in the adaptation to glucose, controlling cytosolic cAMP levels and consequently the cAMP-dependent protein kinase (PKA) activity.Moreover, Ras signalling has been identified in several pathogenic yeasts as a key controller for virulence, due to its involvement in yeast morphogenesis. Nowadays, yeasts are still useful for Ras-like proteins investigation, both as model organisms and as a test tube to study variants of heterologous Ras-like proteins.

Calcium is one of the most important second messengers in all eukaryotic cells and, specifically, in budding yeast it plays essential roles in regulating many fundamental cellular processes, such as cell cycle, mating, glucose sensing, salt stress resistance, and cell survival. Like all eukaryotic cells, yeast cells actively maintain their cytosolic free Ca2+ concentration ([Ca2+]i) at extremely low levels, in the range of 50-200 nM, through a finely regulated homeostasis mechanism. Different stimuli can trigger an increase in [Ca2+]i, through calcium influx and/or calcium release from intracellular stores such as vacuoles or ER compartments. For example, glucose addition to nutrient-deprived cells induces a rapid and transient increase in the cytosolic Ca2+ level, largely dependent on an influx of calcium from the extracellular environment but also involving an IP3-dependent calcium release from intracellular stores. Conversely, hypotonic shock induces an increase in [Ca2+]i, mainly mediated by calcium release from intracellular stores, and partially by calcium influx through Cch1 channels on the plasma membrane. In the last few years, calcium signaling research in yeast has benefited from the development of in vivo bioluminescent assays based on the aequorin bioluminescent protein to monitor [Ca2+]i changes, allowing the investigation of known calcium channels and of still unidentified putative Ca2+ transporters.

In budding yeast calcium is an important second messenger involved in controlling many fundamental cellular processes. Hypotonic shock in S. cerevisiae triggers a raise in cytosolic Ca2+ that seems to depend both on calcium influx and on calcium release from internal stores. Calcium signal is still present in strains carrying the deletion of all known calcium channels, allowing us to suppose the involvement of still unknown calcium channel. Computational data (JBC 2002 277:31079–88) suggested to consider Yor365c and Yal053w, two putative TRP ion channels. Surprisingly, during the response to hypotonic shock in YPD growing yeast we did not observe the typical calcium induced calcium release that characterize calcium signalling in response to other stresses but we noticed a great sensitivity to calcium and a higher signal in the absence of extracellular calcium, indicating that calcium raise is due to an intracellular calcium release. Our data suggest that yeast response to hypotonic shock is mediated by Mid1 and Yal053w that release calcium from internal stores and by Cch1 that drives the influx of calcium from extracellular environment.

In S. cerevisiae, PKA pathway controls metabolism, stress resistance and proliferation. PKA is regulated both by Gpr1/Gpa2 system and the small Ras proteins whose activity is finely controlled by Cdc25/Sdc25 guanine nucleotide exchange factors and Ira GTPase activating proteins. Ira1 and Ira2 are homologs of human neurofibromin 1 (NF1) protein, whose mutations were found to be involved in human neurofibromatosis. The yeast RasGAP proteins share similar aminoacids sequence and have related, but not identical,functions. Scaffolding functions associated with the N-terminal non-catalytic large regions of Ira proteins have not been completely characterized, and the suggested feedback regulation improving RasGAP activity is still unclear at the molecular level. The effects of disjunction of Ira proteins functional regions were investigated, by analyzing strains deprived either of the RasGAP domain or of the entire RasGAP protein, or by expressing the isolated RasGAP domain either in the presence or in the absence of the N-terminal region. Surprisingly, uncorrelated effects on cell size and heat shock sensitivity were observed, although both of these traits are classically reported as PKA activity related phenotypes. Finally, the effects on Ras complex components localization inside the cell were evaluated.

Ras proteins function as a point of convergence for different signalling pathways in eukaryotes and are involved in many cellular responses; their different subcellular locations could regulate distinct functions. To investigate the localization of active Ras in vivo in Saccharomyces cerevisiae, we expressed a probe consisting of a GFP fusion with a trimeric Ras binding domain of Raf1 (eGFP-RBD3), which binds Ras-GTP with a much higher affinity than Ras-GDP. Our results show that in wild type cells active Ras accumulates mainly at the plasma membrane and in the nucleus during growth on medium containing glucose, while it accumulates mainly in mitochondria in wild type glucose-starved cells and relocalizes to the plasma membrane and to the nucleus upon addition of this sugar. A similar pattern is observed in a strain deleted in the CYR1 gene indicating that the absence of adenylate cyclase does not impair the localization of Ras-GTP. Remarkably, in a gpa2 Delta, but not in a gpr1 Delta mutant, active Ras accumulates in internal membranes and mitochondria, both when cells are growing on glucose medium or are starved, indicating that Gpa2, but not Gpr1 is required for the recruitment of Ras-GTP at the plasma membrane and in the nucleus. Moreover, deletion of both HXK1 and HXK2 also causes a mitochondrial localization of the probe, which relocalizes to the plasma membrane and to the nucleus upon expression of HXK2 on a centromeric plasmid, suggesting that this kinase is involved in the proper localization of active Ras. (C) 2012 Elsevier Ltd. All rights reserved.

Using an eGFP-RBD3 probe, which specifically binds Ras-GTP, we recently showed that the fluorescent probe was localized to the plasma membrane and to the nucleus in wild type cells growing exponentially on glucose medium, indicating the presence of active Ras in these cellular compartments. To investigate the nuclear function of Ras-GTP, we generated a strain where Ras2 is fused to the nuclear export signal (NES) from the HIV virus, in order to exclude this protein from the nucleus. Our results show that nuclear active Ras2 is required for invasive growth development in haploid yeast, while the expression of the NES-Ras2 protein does not cause growth defects either on fermentable or non-fermentable carbon sources and does not influence protein kinase A (PKA) activity related phenotypes analysed. Moreover, we show that the cAMP/PKA pathway controls invasive growth influencing the localization of active Ras. In particular, we show that PKA activity plays a role in the localization of active Ras and influences the ability of the cells to invade the agar: high PKA activity leads to a predominant nuclear accumulation of active Ras and induces invasive growth, while low PKA activity leads to plasma membrane localization of active Ras and to a defective invasive growth phenotype.

Ral GTPases have been implicated in tumorigenesis and metastasis in vitro and animal models; furthermore Ral pathway appears to play a prominent role in transformation of human cells (Smith et al. 2007 Clin. Cancer Res. 13, 3803-3813). RalGPS2 is a GEF for RalA belonging to RalGPS family that contains a well conserved Ras-GEF domain, a PxxP motif and a PH domain. Previous experiments demonstrated that RalGPS2 activates RalA in vivo, while its PH-PxxP domain acts as a dominant negative for RalA activation in NIH3T3 and PC12 cells. These data suggest that RalGPS2 PH-PxxP domain could inhibit RalA activation influencing cytoskeleton rearrangements. The aim of this project is to analyse the role of RalGPS2 and of its PH-PxxP domain in human bladder cancer cells (5637) and rodent transformed cells (NIH3T3-k-Ras). RalA and RalGPS2 were highly expressed in 5637 cells and the overexpression of PH-PxxP domain reduced the level of RalA-GTP. Besides the overexpression of PH and PH-PxxP domains in both cell lines induced a marked cytoskeleton re-organization: in particular the PH domain caused formation of thin vesiculating protrusion while the PH-PxxP domain caused formation of long inter-cellular structure probably involved in the exchange of signals and cellular components between cells.

In Saccharomyces cerevisiae, cAMP/pKA pathway plays a major role in metabolism, stress resistance and proliferation control. cAMP is produced by adenylate cyclase, which is activated both by Gpr1/Gpa2 system and Ras proteins, regulated by Cdc25/Sdc25 guanine exchange factors and Ira GTPase activator proteins. Recently, both Ras2 and Cdc25 RasGEF were reported to localize not only in plasma membrane but also in internal membranes. Here, the subcellular localization of Ras signaling complex proteins was investigated both by fluorescent tagging and by biochemical cell membrane fractionation on sucrose gradients. Although a consistent minor fraction of Ras signaling complex components was found in plasma membrane during exponential growth on glucose, Cdc25 appears to localize mainly on ER membranes, while Ira2 and Cyr1 are also significantly present on mitochondria. Moreover, PKA Tpk1 catalytic subunit overexpression induces Ira2 protein to move from mitochondria to ER membranes. These data confirm the hypothesis that different branches of Ras signaling pathways could involve different subcellular compartments, and that relocalization of Ras signaling complex components is subject to PKA control.

Previous work from our laboratories demonstrated that the sugar-induced activation of plasma membrane H(+)-ATPase in Saccharomyces cerevisiae is dependent on calcium metabolism with the contribution of calcium influx from external medium. Our results demonstrate that a glucose-induced calcium (GIC) transporter, a new and still unidentified calcium carrier, sensitive to nifedipine and gadolinium and activated by glucose addition, seems to be partially involved in the glucose-induced activation of the plasma membrane H(+)-ATPase. On the other hand, the importance of calcium carriers that can release calcium from internal stores was analyzed in glucose-induced calcium signaling and activation of plasma membrane H(+)-ATPase, in experimental conditions presenting very low external calcium concentrations. Therefore the aim was also to investigate how the vacuole, through the participation of both Ca(2+)-ATPase Pmc1 and the TRP homologue calcium channel Yvc1 (respectively, encoded by the genes PMC1 and YVC1) contributes to control the intracellular calcium availability and the plasma membrane H(+)-ATPase activation in response to glucose. In strains presenting a single deletion in YVC1 gene or a double deletion in YVC1 and PMC1 genes, both glucose-induced calcium signaling and activation of the H(+)-ATPase are nearly abolished. These results suggest that Yvc1 calcium channel is an important component of this signal transduction pathway activated in response to glucose addition. We also found that by a still undefined mechanism Yvc1 activation seems to correlate with the changes in the intracellular level of IP(3). Taken together, these data demonstrate that glucose addition to yeast cells exposed to low external calcium concentrations affects calcium uptake and the activity of the vacuolar calcium channel Yvc1, contributing to the occurrence of calcium signaling connected to plasma membrane H(+)-ATPase activation.

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway plays a major role in the regulation of metabolism, stress resistance and cell cycle progression. We extend here a mechanistic model of the Ras/cAMP/PKA pathway that we previously defined by describing the molecular interactions and post-translational modifications of proteins, and perform a computational analysis to investigate the dynamical behaviors of the components of this pathway, regulated by different control mechanisms. We carry out stochastic simulations to consider, in particular, the effect of the negative feedback loops on the activity of both Ira2 (a Ras-GAP) and Cdc25 (a Ras-GEF) proteins. Our results show that stable oscillatory regimes for the dynamics of cAMP can be obtained only through the activation of these feedback mechanisms, and when the amount of Cdc25 is within a specific range. In addition, we highlight that the levels of guanine nucleotides pools are able to regulate the pathway, by influencing the transition between stable steady states and oscillatory regimes.

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regulated by multiple feedback loops, exerted by the protein kinase A (PKA) on a few pivotal components of the pathway. In this article, we investigate the dynamics of the second messenger cAMP by performing stochastic simulations and parameter sweep analysis of a mechanistic model of the Ras/cAMP/PKA pathway, to determine the effects that the modulation of these feedback mechanisms has on the establishment of stable oscillatory regimes. In particular, we start by studying the role of phosphodiesterases, the enzymes that catalyze the degradation of cAMP, which represent the major negative feedback in this pathway. Then, we show the results on cAMP oscillations when perturbing the amount of protein Cdc25 coupled with the alteration of the intracellular ratio of the guanine nucleotides (GTP/GDP), which are known to regulate the switch of the GTPase Ras protein. This multi-level regulation of the amplitude and frequency of oscillations in the Ras/cAMP/PKA pathway might act as a fine tuning mechanism for the downstream targets of PKA, as also recently evidenced by some experimental investigations on the nucleocytoplasmic shuttling of the transcription factor Msn2 in yeast cells.

In Saccharomyces cerevisiae the Cdc25/Ras/cAMP pathway is involved in cell growth and proliferation regulation. Ras proteins are regulated by Ira1/2 GTPase activating proteins (GAPs) and Cdc25/Sdc25 guanine nucleotide exchange factors (GEFs). Most of cytosolic Cdc25 protein was found on internal membranes in exponentially growing cells, while upon incubation in a buffer with no nutrients it is re-localized to plasma membrane. The overexpression of Tpk1 PKA catalytic subunit also induces Cdc25 export from the nucleus, involving two serine residues near the Nuclear Localization Site (NLS): mutation of Ser 825 and Ser 826 to glutamate is sufficient to exclude physiologically expressed Cdc25 from the nucleus, mimicking Tpk1 overproduction effect. Mutation of these Ser residues to Ala abolishes the effect of nuclear export induced by Tpk1 overexpression on a Cdc25eGFP fusion. Moreover, mutation of these residues affects PKA-related phenotypes such as heat shock resistance, glycogen content and cell volume. © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Ral proteins are members of the Ras GTPase superfamily and localize at the plasma membrane, in endocytic and exocytic vesicles and in synaptic vesicles. These GTPases are involved in multiple cellular events including proliferation, migration, differentiation, cytoskeletal organization, vesicular transport, exocytosis and receptor endocytosis. They are also implicated in tumorigenesis, invasion and metastasis. RalGPS2 is a guanine nucleotide exchange factor for RalA belonging to RalGPS family. It is a 590 aminoacids polypeptide that contains a well conserved Ras-GEF domain, a PxxP motif and a PH (Pleckstrin Homology) domain. Previous experiments have demonstrated that RalGPS2 can activate RalA in vivo, while the PH-PxxP domain acts as a dominant negative for RalA activation in both NIH3T3 and PC12 cells. These data suggest that the PH-PxxP domain of RalGPS2 could inhibit RalA activation, thus influencing cytoskeleton rearrangement. The principal aim of this work is to analyze the role of RalGPS2 and of its PH-PxxP domain in human and rodent cells transformation. In particular our attention was been focused on transformed murine fibroblasts (NIH3T3 k-Ras) and on human bladder cancer cells (5637 cell line). We found that RalA and RalGPS2 were highly expressed in 5637 human bladder cancer cells and that the overexpression of PHPxxP domain reduced the level of active RalA bound at GTP. Furthermore the expression of PH and PH-PxxP domains in both NIH3T3 k-ras and 5637 cell line, induced a marked cytoskeleton re-organization. In particular PH domain caused formation of thin protrusions with the presence of vesicles. PH-PxxP domain caused formation of long inter-cellular structure that are probably involved in the exchange of signals and cellular components between different cells. It will be interesting in the future to understand the molecular nature of these ‘‘hairy’’ structures that could be nanotubes.

The vesicular trafficking inside eukaryotic cells is a highly regulated process that requires specificity at each transport step. The selective interaction between donor and acceptor membranes is mediated by tethering factors, among which GARP (Golgi associated retrograde protein) complex. The vacuolar protein sorting Vps54 is a subunit of GARP and in yeast is involved in the retrograde transport of early endosomes to the trans Golgi network. In the mouse, a single point mutation near the C-terminus of Vps54 (L967Q) gives rise to the Wobbler phenotype, characterized by defects in motor neuron function and male sterility. We took advantage of this mutant variant to investigate more in detail the role of Vps54 in vesicular trafficking of mammalian cells. In cultured HEK293 cells, Vps54-GFP colocalizes with Golgi and partially with endosomal compartment. The localization of the wobbler variant is comparable with that of wt protein, even if Vps54L967Q-GFP is slightly more diffuse into the cytoplasm. This result supports the literature data suggesting that wobbler Vps54 retains activity in trafficking. Since wobbler disease specifically affects spermatogenesis, we focused our attention on Vps54 in developing mouse germ cells. In the physiological contest, we demonstrated that Vps54 is involved in acrosome biogenesis. The acrosome is an acidic vesicle of not better-identified origin, indispensable for fertilization. Wobbler spermatozoa are resulted to lack a true acrosome: during sperm cell differentiation Vps54(L967Q) marks numerous punctuated vesicles that, on the contrary of the wt Vps54-labeled ones, are not able to coalesce and develop into the acrosome. These results were confirmed by double immunostaining with USP8, a deubiquitinating enzyme marker of the endocytic pathway. We investigated by exploiting recombinant proteins if the absence of an acrosome could depend on the failure of Vps54L967Q to interact with sperm factors involved in trafficking machinery

In S. cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regulated by multiple feedback loops that can lead the second messenger cAMP to oscillatory regimes. In this paper we analyze the dynamics of cAMP by performing stochastic simulations of a mechanistic model of the Ras/cAMP/PKA pathway, to consider the effects of the deletion of phosphodiesterases (the enzymes catalyzing the degradation of cAMP, which represent the major negative feedback in this pathway) and the role of the intracellular ratio of guanine nucleotides (GTP/GDP).

Glucose addition to glucose-starved Saccharomyces cerevisiae cells triggers a quick and transient influx of calcium from the extracellular environment. In yeast at least two different carrier systems were identified: a high affinity system, requiring Cch1 channel, and a low affinity system. Here we report that another calcium transport system exists in yeast, not yet identified, that can substitute the two known systems when they are inactivated. This system was called GIC (for Glucose Induced Calcium) system and it is a high affinity calcium transport system, magnesium-sensitive but nickel-resistant. Moreover, GIC transport is sensitive to gadolinium and nifedipine, but it is not sensitive to inhibition by verapamil, which conversely behaves as an agonist on glucose response.GIC transport is fully functional in conditions when calcineurin is active, a serine/threonine specificity phosphatase involved in the regulation of calcium homeostasis and in many other cellular phenomena such as tolerance to high concentrations of Na+ and Li+, response to pheromones and gene transcription regulation. Here it is reported for the first time that calcineurin can also be activated by nutrients: the activation of Crz1 transcription factor by calcineurin was observed in derepressed cells after addition of glucose in the presence of extracellular calcium. © 2011 Elsevier Ltd.

This paper reports the synthesis of a panel of small molecules with arylamides and arylsulfonamides groups and their biological activity in inhibiting nucleotide exchange on human Ras. The design of these molecules was guided by experimental and molecular modelling data previously collected on similar compounds. Aim of this work is the validation of the hypothesis that a phenyl hydroxylamine group linked to a second aromatic moiety generates a pharmacophore capable to interact with Ras and to inhibit its activation. In vitro experiments on purified human Ras clearly show that the presence of an aromatic hydroxylamine and a sulfonamide group in the same molecule is a necessary condition for Ras binding and nucleotide exchange inhibition. The inhibitor potency is lower in molecules in which either the hydroxylamine has been replaced by other functional groups or the sulfonamide has been replaced by an amide. In the case both these moieties, the hydroxylamine and sulfonamide are absent, inactive compounds are obtained.

RalGPS2 is a guanine nucleotide exchange factor for RalA GTPase characterized by a C-terminal Pleckstrin Homology (PH) domain; this GEF is endogenously expressed in PC12 cells and in rat brain but its role in PC12 cells and in cell differentiation is actually unknown. Here we have shown that transient expression of RalGPS2-PH-PxxP domain in PC12 and PC12-TrkA cells induces high level of neurite outgrowth; this differentiation is comparable with that of PC12 cells treated with RalGPS2 siRNA. Stable PC12 cell lines expressing the PH-PxxP domain of RalGPS2 have been generated; in these cell lines the PH-PxxP domain acts as a dominant negative for RalA activation, promotes cells differentiation and re-directs NGF signals towards MAPKs. Furthermore it has been also demonstrated that the PH-PxxP domain of RalGPS2 induces microspikes formation a typical feature of cells in which the Cdc42 GTPase is constitutively activated.

Mutation of RAS genes is a critical event in the pathogenesis of different human tumors and in some developmental disorders. Here we present an arabinose-derived bicyclic compound displaying selective cytotoxicity in human colorectal cancer cells expressing K-RasG13D, that shows high intrinsic nucleotide exchange rate. We characterize binding of bicyclic compounds by docking and NMR experiments and their inhibitory activity on GEF-mediated nucleotide exchange on wild-type and mutant Ras proteins. We demonstrate that the in vitro inhibition of Ras nucleotide exchange depends on the molar ratio between Ras and its GEF activator, suggesting that the observed in vivo selective effect may depend on biochemical parameters and actual intracellular concentration of the Ras protein and its regulators

The brain-specific Ras guanine nucleotide exchange factor RasGRF1 is a protein harbouring a complex array of structural motifs. It contains a pleckstrin homology (PH1) domain, a coiled coil region (CC) and an ilimaquinone (IQ) one in addition to the catalytic Ras and Rac exchange factor domains. In this study, we used the recombinant N-terminal PH1, CC and IQ region (PHCCIQ) fused to the chitin-binding domain to isolate interacting proteins from mouse brain extracts. The use of an advanced software tool, the Pep-Miner, allowed clustering similar spectra from multiple mass spectrometry analysis, simplifying and improving the analysis of the complex peptide mixture. The most representative classes of RasGRF1-interacting proteins were ribosomal and other RNA-binding proteins, cytoskeletal proteins and proteins involved in vesicular trafficking. We confirmed the interaction of some of the identified proteins using different experimental approaches. We also demonstrated an RNA-dependent association of the PHCCIQ moiety of RasGRF1 with ribosomal protein S6 and Ras-GTPase-activating protein SH3-domain binding protein 2. In addition, we found that purified total RNA binds to the PHCCIQ fusion protein and the recombinant protein associates with poly(A)-sepharose. These data indicate that RasGRF1 can interact with different protein categories and exhibits a potential RNA-binding property. © 2008 Humana Press.

A panel of new potential Ras ligands was generated by decorating a tricyclic levoglucosenone-derived scaffold with aromatic moieties. Some members of the panel showed in vitro activity in inhibiting the nucleotide exchange on Ras and were toxic for some human cancer cell lines

The mechanisms regulating the activity of Saccharomyces cerevisiae Ras-GEF Cdc25 are still largely unknown. While the catalytical function of the C-terminal domain has been thoroughly studied, only recently a role of negative control on the protein activity has been suggested for the dispensable N-terminal domain. In order to investigate Cdc25 localization and the role of its different domains, several fusion proteins were constructed using the full length Cdc25 or different fragments of the protein with the green fluorescent protein. Unexpectedly, even if only slightly overexpressed, the full protein was not located in the cell plasma membrane, but accumulates inside the cell and also into the nucleus. Moreover, the endogenous Cdc25, tagged with HA, was also found in purified nuclear extracts. The fusions spanning aa 353-875, aa 876-1100 or aa 353-1100 localize heavily in the nucleus, concentrating in the nuclear peripheral area, in a region distinct from the nucleolus. This could be related to the presence of two predicted nuclear localization signals (NLS) in positions 547 and 806, but also to the contribution of another region, spanning residues 876-1100. This localization is likely to be physiological, since the fusion proteins can be efficiently exported and then imported back into the nucleus

In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of metabolism and cell cycle progression. The pathway is tightly regulated by several control mechanisms, as the feedback cycle ruled by the activity of phosphodiesterase. Here, we present a discrete mathematical model for the Ras/cAMP/PKA pathway that considers its principal cytoplasmic components and their mutual interactions. The tau-leaping algorithm is then used to perform stochastic simulations of the model. We investigate this system under various conditions, and we test how different values of several stochastic reaction constants affect the pathway behaviour. Finally, we show that the level of guanine nucleotides, GTP and GDP, could be relevant metabolic signals for the regulation of the whole pathway. © 2007 Elsevier B.V. All rights reserved.

The plasma membrane H(+)-ATPase from Saccharomyces cerevisiae is an enzyme that plays a very important role in the yeast physiology. The addition of protonophores, such as 2,4-dinitrophenol (DNP) and carbonyl cyanide m-chlorophenylhydrazone (CCCP), also triggers a clear in vivo activation of this enzyme. Here, we demonstrate that CCCP-induced activation of the plasma membrane H(+)-ATPase shares some similarities with the sugar-induced activation of the enzyme. Phospholipase C and protein kinase C activities are essential for this activation process while Gpa2p, a G protein involved in the glucose-induced activation of the ATPase, is not required. CCCP also induces a phospholipase C-dependent increase in intracellular calcium. Moreover, we show that the availability of extracellular calcium is required for CCCP stimulation of H(+)-ATPase, suggesting a possible connection between calcium signaling and activation of ATPase.

Autophosphorylation of tyrosine residues on the cytoplasmic tail of the epidermal growth factor receptor ( EGFR) upon ligand binding leads to recruitment of the Grb2/Sos complex to the activated receptor and to activation of the Ras pathway. The major aim of this study was to ascertain to which extent the EGFR module ( receptor, Grb2, hSos1) could work in a lower eukaryote, completely devoid of tyrosine kinase receptors but possessing hortologues to mammalian Ras proteins. We show that the EGFR module can be functionally linked to the Ras/cAMP pathway in a Saccharomyces cerevisiae cdc25(ts) strain, as monitored by several independent biological readouts, including drop of budding index, decrease of cAMP level and acquisition of thermotolerance. Autophosphorylation of the receptor is a necessary step for RTK-dependent activation of the yeast Ras pathway, since genetic and pharmacological downregulation of the EGFR catalytic activity abolish coupling with the Ras/cAMP pathway. Thus, our results newly indicate that a RTK-based signal transduction module can be functionally coupled to the yeast Ras/cAMP pathway and that our system can be a valuable tool for the screen of drugs inhibiting the kinase activity of the receptor.

In this communication the ability of new compound to inhibit nucleotide exchange on human Ras through STD NMR experiments is presented. Interestingly, the Surface Plasmon Resonance (SPR) studies reported here demonstrate for the first time that both glucose-derived and arabinose-derived compounds inhibit the interaction between Ras and the Guanine nucleotide Exchange Factor protein (C-Cdc25). This experimental evidence contributes to explain at a molecular level the mode of action of our inhibitors. Too complex to change. New glucose-derived phenylhydroxylamines inhibit nucleotide exchange on human Ras. NMR and SPR experiments indicated that the Ras-GEF interaction is inhibited when the Ras-ligand complex is formed. (Chemical Equation Presented). © 2007 Wiley-VCH Verlag GmbH & Co. KGaA.

The Saccharomyces cerevisiae CDC25 gene encodes a guanine nucleotide exchange factor for Ras proteins whose catalytic domain is highly homologous to Ras-guanine nucleotide exchange factors from higher eukaryotes. In this study, glucose-induced Ras activation and cAMP response were investigated in mutants lacking the N-terminal domain of Cdc25 or where the entire CDC25 coding sequence was substituted by an expression cassette for a mammalian guanine nucleotide exchange factor catalytic domain. Our results suggest that an unregulated, low Ras guanine nucleotide exchange factor activity allows a normal glucose-induced cAMP signal that appears to be mediated mainly by the Gpr1/Gpa2 system, but it was not enough to sustain the glucose-induced increase of Ras2-GTP normally observed in a wild-type strain.

RalGPS2 is a murine guanine nucleotide exchange factor of the RalGPS family; it contains a Cdc25-like GEF domain and does not exhibit a Ras-binding domain. The main characteristic of RalGPS2 is its pleckstrin homology (PH) domain, present at the C terminus, that preferentially binds phosphatidylinositol-4,5-biphosphate and in HEK 293 cells localized in membranes, causing ruffling and vesiculation. Moreover, RalGPS2 contains a PxxP motif in the central part of the molecule. This motif binds in vitro and in vivo SH3 domains of Grb2 and PLCgamma. RalGPS2 and its GEF domain activate RalA in vivo while the PH-PxxP domains inhibited it behaving as a dominant negative for the RalA pathway; this activation was not inhibited by co-expression of a dominant negative Ras. RalGPS2 is physiologically expressed in testis and brain; when overexpressed, the whole RalGPS2 causes considerable morphological changes in HEK 293 cells, suggesting its possible role on cytoskeleton reorganization. This is further strengthened by data obtained in NIH3T3 cells where expression of PH-PxxP domain promotes actin depolymerization. Finally, RalGPS2 and its GEF domain induce Ras-independent transcriptional activation of the c-fos promoter in NIH3T3 cells.

Novel inhibitors of Ras protein activation have been found, containing a bicyclic core derived from D-arabinose and benzyl and phenylhydroxylamine moieties. NMR studies (trNOE, saturation-transfer difference, STD) of the binding between these molecules and human p21 h-Ras are reported. A pharmacophore mapping indicates that both the benzyl and the phenylhydroxylamine moieties are essential for protein binding. Molecules lacking one of these groups were synthesized and tested to confirm this hypothesis, and no interaction with Ras in vitro, nor biological activity in mammalian cells was observed. Our studies led to the development of molecules that selectively inhibit Ras-dependent cellular growth in mammalian cells. © Wiley-VCH Verlag GmbH & Co. KGaA, 2006.

In the yeast Saccharomyces cerevisiae, the Cdc25/Ras/cAMP/protein kinase A (PKA) pathway plays a major role in the control of metabolism, stress resistance and proliferation, in relation to the available nutrients and conditions. The budding yeast RasGEF Cdc25 was the first RasGEF to be identified in any organism, but very little is known about its activity regulation. Recently, it was suggested that the dispensable N-terminal domain of Cdc25 could negatively control the catalytic activity of the protein. In order to investigate the role of this domain, strains were constructed that produced two different versions of the C-terminal domain of Cdc25 (aa 907–1589 and 1147–1589). The carbon-source-dependent cell size control mechanism present in the wild type was found in the first of these mutants, but was lost in the second mutant, for which the cell size, determined as protein content, was the same during exponential growth in both ethanol- and glucose-containing media. A biparametric analysis demonstrated that this effect was essentially due to the inability of the mutant producing the shorter sequence to modify its protein content at budding. A similar phenotype was observed in strains that lacked CDC25, but which possessed a mammalian GEF catalytic domain. Taken together, these results suggest that Cdc25 is involved in the regulation of cell size in the presence of different carbon sources. Moreover, production of the aa 876–1100 fragment increased heat-stress resistance in the wild-type strain, and rescued heat-shock sensitivity in the ira1 delta background. Further work will aim to clarify the role of this region in Cdc25 activity and Ras/cAMP pathway regulation.

In this work, we show that glucose-induced activation of plasma membrane H+-ATPase from Saccharomyces cerevisiae is strongly dependent on calcium metabolism and that the glucose sensor Snf3p works in a parallel way with the G protein Gpa2p in the control of the pathway. The role of Snf3p is played by the Snf3p C-terminal tail, since in a strain with the deletion of the SNF3 gene, but also expressing a chimera protein formed by Hxt1p (a glucose transporter) and the Snf3p C-terminal tail, a normal glucose-activation process can be observed. We present evidences indicating that Snf3p would be the sensor for the internal signal (phosphorylated sugars) of this pathway that would connect calcium signaling and activation of the plasma membrane ATPase. We also show that Snf3p could be involved in the control of Pmc1p activity that would regulate the calcium availability in the cytosol.

The mouse USP8/mUBPy gene codifies a deubiquitinating enzyme expressed preferentially in testis and brain. While the ubiquitin-specific processing proteases (UBPs) are known to be important for the early development in invertebrate organisms, their specific functions remain still unclear in mammals. Using specific antibodies, raised against a recombinant mUBPy protein, we studied mUBPy in mouse testis. The mUBPy is expressed exclusively by the germ cell component and is maintained in epididymal spermatozoa. The enzyme is functionally active, being able to detach ubiquitin moieties from endogenous protein substrates. Protein interaction assays showed that sperm UBPy interacts with MSJ-1, the sperm-specific DnaJ protein evolutionarily conserved for spermiogenesis. Immunocytochemistry revealed that mUBPy shares with MSJ-1 the intracellular localization during spermatid cell differentiation; intriguingly, we show here that the proteasomes also locate in mUBPy/MSJ-1-positive sites, such as the cytoplasmic surface of the developing acrosome and the centrosomal region. These colocalization sites are maintained in epididymal spermatozoa. The demonstration of a protein interaction between a deubiquitinating enzyme and a molecular chaperone and the documentation on the proteasomes in both differentiating and mature mouse male germ cells suggest that members of the chaperone and ubiquitin/proteasome systems could cooperate in the fine control of protein quality to yield functional spermatozoa.

Recombinant human nerve growth factor (rhNGF) is regarded as the most promising therapy for neurodegeneration of the central and peripheral nervous systems as well as for several other pathological conditions involving the immune system. However, rhNGF is not commercially available as a drug. In this work, we provide data about the production on a laboratory scale of large amounts of a rhNGF that was shown to possess in vivo biochemical, morphological, and pharmacological effects that are comparable with the murine NGF (mNGF), with no apparent side effects, such as allodynia. Our rhNGF was produced by using conventional recombinant DNA technologies combined with a biotechnological approach for high-density culture of mammalian cells, which yielded a production of approximately 21.5 +/- 2.9 mg/liter recombinant protein. The rhNGF-producing cells were thoroughly characterized, and the purified rhNGF was shown to possess a specific activity comparable with that of the 2.5S mNGF by means of biochemical, immunological, and morphological in vitro studies. This work describes the production on a laboratory scale of high levels of a rhNGF with in vitro and, more important, in vivo biological activity equivalent to the native murine protein

The design and synthesis of novel Ras inhibitors with a bicyclic scaffold derived from the natural sugar D-arabinose are presented. Molecular modelling showed that these ligands can bind Ras by accommodating the aromatic moieties and the phenylhydroxylamino group in a cavity near the Switch II region of the protein. All the synthetic compounds were active in inhibiting nucleotide exchange on p21 human Ras in vitro, and two of them selectively inhibited Ras-dependent cell growth in vivo. © 2005 Wiley-VCH Verlag GmbH & Co. KGaA.

The Ras proteins, which regulate intracellular signaling by a cyclic process involving interconversion between active GTP-bound and inactive GDP-bound states, play an essential role in controlling the activity of several crucial signaling pathways regulating normal cellular proliferation. Mutational activation of RAS genes can induce cancer in humans and other mammals. About 30% of human tumors contain an altered oncogenic Ras; therefore, inhibitors of Ras activation are potentially antineoplastic drugs. In this work we describe original molecules acting as Ras inhibitors. Recently a new class of inhibitors of the Ras nucleotide exchange process was described by Taveras et al. These molecules are able to form a noncovalent complex with Ras-GDP, inhibiting the GDP-GTP nucleotide exchange. We synthesized molecule SCH-53870 and we found that it inhibits p21-hRas nucleotide exchange in vitro, but it has very low solubility in water and undergoes rapid degradation at room temperature when dissolved in water-DMSO mixtures. This chemical instability could prejudice pharmacological activity in vivo. With the aim to improve solubility and chemical stability, we designed and synthesized other original bioactive molecules that have been characterized in vitro using purified human and yeast Ras proteins and in vivo using suitable Saccharomyces cerevisiae strains. In the long term we hope that the knowledge we derive from these compounds will help in the development of an alternative therapy targeting Ras for a specific inhibition of transformed cell proliferation. © 2004 New York Academy of Sciences.

The Saccharomyces cerevisiae phospholipase C Plc1 is involved in cytosolic transient glucose-induced calcium increase, which also requires the Gpr1/Gpa2 receptor/G protein complex and glucose hexokinases. Differing from mammalian cells, this increase in cytosolic calcium concentration is mainly due to an influx from the external medium. No inositol triphosphate receptor homologue has been identified in the S. cerevisiae genome; and, therefore, the transduction mechanism from Plc1 activation to calcium flux generation still has to be identified. Inositol triphosphate (IP3) in yeast is rapidly transformed into IP4 and IP5 by a dual kinase, Arg82. Then another kinase, Ipk1, phosphorylates the IP5 into IP6. In mutant cells that do not express either of these kinases, the glucose-induced calcium signal was not only detectable but was even wider than in the wild-type strain. IP3 accumulation upon glucose addition was completely absent in the plc1Delta strain and was amplified both by deletion of either ARG82 or IPK1 genes and by overexpression of PLC1. These results taken together suggest that Plc1p activation by glucose, leading to cleavage of PIP2 and generation of IP3, seems to be sufficient for raising the calcium level in the cytosol. This is the first indication for a physiological role of IP3 signalling in S. cerevisiae. Many aspects about the signal transduction mechanism and the final effectors require further study.

Wide genome analysis of difference in gene expression between spermatogonial populations from 7-day-old mice and pachytene spermatocytes from 18-day-old mice was performed using Affymetrix gene chips representing similar to 12,500 mouse known genes or EST sequences. spanning approximately 1/3rd of the mouse genome. To delineate differences in the profile of gene expression between mitotic and meiotic stages of male germ cell differentiation, expressed genes were grouped in functional clusters. The analysis confirmed the previously described pre-meiotic or meiotic expression for several genes, in particular for those involved in the regulation of the mitotic and meiotic cell cycle. and for those whose transcripts are accumulated during the meiotic stages to be translated later in post-meiotic stages. Differential expression of several additional genes was discovered. In few cases (pro-apoptotic factors Bak, Bad and Bax), data were in conflict with the previously published stage-dependent expression of genes already known to be expressed in male germ cells. Northern blot analysis of selected genes confirmed the results obtained with the microarray chips. Six of these were novel genes specifically expressed in pachytene spermatocytes: a chromatin remodeling factor (chrac1/YCL1). a homeobox gene (hmx1), a novel G-coupled receptor for an unknown ligand (Gpr19), a glycoprotein of the intestinal epithelium (mucin 3), a novel RAS activator (Ranbp9), and the A630056B21Rik gene (predicted to encode a novel zinc finger protein). These studies will help to delineate the global patterns of gene expression characterizing male germ cell differentiation for a better understanding of regulation of spermatogenesis in mammals. (C) 2003 Elsevier B.V. All rights reserved.