Sphingoid Base Metabolism in Yeast: Mapping Gene Expression Patterns Into Qualitative Metabolite Time Course Predictions

Can qualitative metabolite time course predictions be inferred from measured mRNA expression patterns? Speaking against this possibility is the large number of ‘decoupling’ control points that lie between these variables, i.e. translation, protein degradation, enzyme inhibition and enzyme activation. Speaking for it is the notion that these control points might be coordinately regulated such that action exerted on the mRNA level is informative of action exerted on the protein and metabolite levels. A simple kinetic model of sphingoid base metabolism in yeast is postulated. When the enzyme activities in this model are modulated proportional to mRNA expression levels measured in heat shocked yeast, the model yields a transient rise and fall in sphingoid bases followed by a permanent rise in ceramide. This finding is in qualitative agreement with experiments and is thus consistent with the aforementioned coordinated control system hypothesis

Coordination of MAP Kinase Signaling During Cell Fate Decisions

Cells detect and respond to a wide diversity of environmental signals. These signals commonly stimulate mitogen-activated protein kinase (MAPK) pathways that evoke a cellular response. Particular environmental signals generate MAPK responses that are mutually exclusive. The coordination of competing MAPK signals is required to produce an appropriate cell fate. Budding yeast, Saccharomyces cerevisiae, use MAPK pathways to respond to developmental signals and environmental stress. Mating pheromones initiate the mating response pathway, which promotes mating differentiation. Hyperosmotic stress initiates the high osmolarity stress (HOG) response pathway, which promotes stress adaptation. The two pathways share components despite producing competing cell fates. Here we describe mechanisms that coordinate MAPK signaling to ensure proper cell fate decisions. We studied how the mating MAPK Fus3 and the HOG MAPK, Hog1 are coordinated in co-stimulated cells. We find that stress adaptation takes precedence over mating differentiation by two Hog1-dependent mechanisms. First, Hog1 phosphorylates the protein kinase, Rck2, and thereby inhibits pheromone-induced protein translation. Second, Hog1 phosphorylates a shared pathway component, Ste50, and thereby dampens pheromone-induced MAPK activation. These findings point to two mechanisms of cross-pathway inhibition used by one MAPK to coordinate the activity of a second, competing MAPK. We also studied the coordination that occurs between the two MAPKs activated by mating pheromones, Fus3 and Kss1. Both MAPKs have roles in mating however Kss1 also promotes filamentous growth in response to poor nutrient conditions. Thus, coordination of Fus3 and Kss1 is critical to maintaining proper mating differentiation. We find that Fus3 phosphorylates a shared pathway component Ste7 to diminish Kss1 activity and prevent aberrant filamentous growth during the mating response. The study of mechanisms that determine cell fate in yeast might provide insights about signal coordination and attenuation in more complex eukaryotic MAPK pathways. Our analysis reveal that feedback phosphorylation of shared components contribute to the coordination of MAPK activity. The insights gained from this work could contribute to discovery of new therapies, specifically for disease where MAPK pathways are hyperactivated.Doctor of Philosoph

Technique for Specifying the Fatty Acid at the SN2 Position of Acylglycerol Lipids

A method for specifying a fatty acid at the sn2 position of acylglycerol lipids including (a) transfecting a vector including the SLC1 gene or a variant thereof into embryonic biological material, and (b) allowing the SLC1 gene to specify the type of fatty acid at the sn2 position of acylglycerol lipids. Also provided for is an isolated SLC1 gene and a probe for its detection

Proper Protein Glycosylation Promotes Mitogen-Activated Protein Kinase Signal Fidelity

The ability of cells to sense and respond appropriately to changing environmental conditions is often mediated by signal transduction pathways that employ mitogen-activated protein kinases (MAPKs). In the yeast Saccharomyces cerevisiae, the high osmolarity glycerol (HOG) and the filamentous growth (FG) pathways are activated following hyperosmotic stress and nutrient deprivation, respectively. Whereas the HOG pathway requires the MAPK Hog1, the FG pathway employs the MAPK Kss1. We conducted a comprehensive screen of nearly 5,000 gene deletion strains for mutants that exhibit inappropriate cross-talk between the HOG and FG pathways. We identified two novel mutants, mnn10Δ and mnn11Δ, that allow activation of Kss1 under conditions that normally stimulate Hog1. MNN10 and MNN11 encode mannosyltransferases that are part of the N-glycosylation machinery within the Golgi apparatus; deletion of either gene results in N-glycosylated proteins that have shorter mannan chains. Deletion of the cell surface mucin Msb2 suppressed the mnn11Δ phenotype, while mutation of a single glycosylation site within Msb2 was sufficient to confer inappropriate activation of Kss1 by salt stress. These findings reveal new components of the N-glycosylation machinery needed to ensure MAPK signaling fidelity

Positive roles for negative regulators in the mating response of yeast

Modeling and experimental analysis of the yeast mating pathway reveals that transcriptional repressor proteins protect a key transcriptional activator from degradation, ensuring that the system is poised to respond rapidly to pheromones and providing a novel mechanism for perfect adaptation.We combine experimentation and mathematical modeling to study the complex interplay between positive and negative regulation of gene expression in the yeast pheromone pathway.The transcriptional repressors Dig1 and Dig2 are shown to have a positive role in mating differentiation by stabilizing the transcriptional activator Ste12. This result was predicted by mathematical modeling and confirmed experimentally.The model also predicts that Ste12 degradation follows saturable kinetics. Again, this observation is confirmed experimentally.The model revealed that stabilization through protein–protein interactions provides a mechanism for robust perfect adaptation and allows the transcriptional response to occur on a time scale that is distinct from upstream signaling events.All cells must detect and respond to changes in their environment, often through changes in gene expression. The yeast pheromone pathway has been extensively characterized, and is an ideal system for studying transcriptional regulation. Here we combine computational and experimental approaches to study transcriptional regulation mediated by Ste12, the key transcription factor in the pheromone response. Our mathematical model is able to explain multiple counterintuitive experimental results and led to several novel findings. First, we found that the transcriptional repressors Dig1 and Dig2 positively affect transcription by stabilizing Ste12. This stabilization through protein–protein interactions creates a large pool of Ste12 that is rapidly activated following pheromone stimulation. Second, we found that protein degradation follows saturating kinetics, explaining the long half-life of Ste12 in mutants expressing elevated amounts of Ste12. Finally, our model reveals a novel mechanism for robust perfect adaptation through protein–protein interactions that enhance complex stability. This mechanism allows the transcriptional response to act on a shorter time scale than upstream pathway activity

Structural, mechanistic and regulatory studies of serine palmitoyltransferase

SLs (sphingolipids) are composed of fatty acids and a polar head group derived from l-serine. SLs are essential components of all eukaryotic and many prokaryotic membranes but S1P (sphingosine 1-phosphate) is also a potent signalling molecule. Recent efforts have sought to inventory the large and chemically complex family of SLs (LIPID MAPS Consortium). Detailed understanding of SL metabolism may lead to therapeutic agents specifically directed at SL targets. We have studied the enzymes involved in SL biosynthesis; later stages are species-specific, but all core SLs are synthesized from the condensation of l-serine and a fatty acid thioester such as palmitoyl-CoA that is catalysed by SPT (serine palmitoyltransferase). SPT is a PLP (pyridoxal 5'-phosphate)-dependent enzyme that forms 3-KDS (3-ketodihydrosphingosine) through a decarboxylative Claisen-like condensation reaction. Eukaryotic SPTs are membrane-bound multi-subunit enzymes, whereas bacterial enzymes are cytoplasmic homodimers. We use bacterial SPTs (e. g. from Sphingomonas) to probe their structure and mechanism. Mutations in human SPT cause a neuropathy [HSAN1 (hereditary sensory and autonomic neuropathy type 1)], a rare SL metabolic disease. How these mutations perturb SPT activity is subtle and bacterial SPT mimics of HSAN1 mutants affect the enzyme activity and structure of the SPT dimer. We have also explored SPT inhibition using various inhibitors (e. g. cycloserine). A number of new subunits and regulatory proteins that have a direct impact on the activity of eukaryotic SPTs have recently been discovered. Knowledge gained from bacterial SPTs sheds some light on the more complex mammalian systems. In the present paper, we review historical aspects of the area and highlight recent key developments.</p

Sphingolipids of the mycopathogen Sporothrix schenckii: identification of a glycosylinositol phosphorylceramide with novel core GlcNH(2)alpha 1 -> 2Ins motif

Acidic glycosphingolipid components were extracted from the yeast form of the dimorphic mycopathogen Sporothrix schenckii. Two minor and the major fraction from the yeast form (Ss-Y1, -Y2, and -Y6. respectively) have been isolated. By a combination of 1- and 2-D H-1-nuclear magnetic resonance (NMR) spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and gas chromatography/mass spectrometry (GC/MS). Ss-Y6 was determined to be triglycosylinositol phosphorylceramide with a novel glycan structure, Man alpha1 --> 3Man alpha1 --> 6GlcNH(2)alpha1 --> 2Ins1-P-1Cer (where Ins = myo-inositol, P = phosphodiester), While the GlcNH(2)alpha1 --> 6Ins1-P-motif is found widely distributed in eukaryotic GPI anchors, the linkage GlcNH(2)alpha1 --> 2Insl-P- has not been previously observed in any glycolipid, Ss-Y1 and Ss-Y2 were both found to have the known glycan structure Man alpha1 --> 3Man alpha1 --> 2Ins1-P-1Cer, Together with the results of a prior study [Toledo et al, (2001) Biochem, Biophys. Res. Commun, 280, 19-24] which showed that the mycelium form expresses GIPCs with the structures Man alpha1 --> 6Ins1-P-1Cer and Man alpha1 --> 3Man alpha1 --> 6Ins1-P-1Cer, these results demonstrate that S, schenckii can synthesize glycosylinositol phosphorylceramides with at least three different core Linkages, (C) 2001 Federation of European Biochemical Societies, Published by Elsevier Science B.V. All rights reserved.Univ Georgia, Dept Biochem & Mol Biol, Athens, GA 30602 USAUniversidade Federal de São Paulo, Escola Paulista Med, Dept Biochem, BR-04023900 São Paulo, BrazilUniv Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USAUniversidade Federal de São Paulo, Escola Paulista Med, Dept Biochem, BR-04023900 São Paulo, BrazilWeb of Scienc

Signal inhibition by a dynamically regulated pool of monophosphorylated MAPK

MAPKs are activated by dual phosphorylation. Much of the MAPK Fus3 is monophosphorylated and acts to inhibit signaling in vivo. Computational models reveal how a kinase scaffold and phosphatase act together to dynamically regulate dual-phosphorylated and monophosphorylated MAPKs and the downstream signal.Protein kinases regulate a broad array of cellular processes and do so through the phosphorylation of one or more sites within a given substrate. Many protein kinases are themselves regulated through multisite phosphorylation, and the addition or removal of phosphates can occur in a sequential (processive) or a stepwise (distributive) manner. Here we measured the relative abundance of the monophosphorylated and dual-phosphorylated forms of Fus3, a member of the mitogen-activated protein kinase (MAPK) family in yeast. We found that upon activation with pheromone, a substantial proportion of Fus3 accumulates in the monophosphorylated state. Introduction of an additional copy of Fus3 lacking either phosphorylation site leads to dampened signaling. Conversely, cells lacking the dual-specificity phosphatase (msg5Δ) or that are deficient in docking to the MAPK-scaffold (Ste5ND) accumulate a greater proportion of dual-phosphorylated Fus3. The double mutant exhibits a synergistic, or “synthetic,” supersensitivity to pheromone. Finally, we present a predictive computational model that combines MAPK scaffold and phosphatase activities and is sufficient to account for the observed MAPK profiles. These results indicate that the monophosphorylated and dual-phosphorylated forms of the MAPK act in opposition to one another. Moreover, they reveal a new mechanism by which the MAPK scaffold acts dynamically to regulate signaling

Combined computational and experimental analysis reveals mitogen-activated protein kinase-mediated feedback phosphorylation as a mechanism for signaling specificity

A series of mathematical models was used to quantitatively characterize pheromone-stimulated kinase activation and determine how mitogen-activated protein (MAP) kinase specificity is achieved. The findings reveal how feedback phosphorylation of a common pathway component can limit the activity of a competing MAP kinase through feedback phosphorylation of a common activator, and thereby promote signal fidelity.Different environmental stimuli often use the same set of signaling proteins to achieve very different physiological outcomes. The mating and invasive growth pathways in yeast each employ a mitogen-activated protein (MAP) kinase cascade that includes Ste20, Ste11, and Ste7. Whereas proper mating requires Ste7 activation of the MAP kinase Fus3, invasive growth requires activation of the alternate MAP kinase Kss1. To determine how MAP kinase specificity is achieved, we used a series of mathematical models to quantitatively characterize pheromone-stimulated kinase activation. In accordance with the computational analysis, MAP kinase feedback phosphorylation of Ste7 results in diminished activation of Kss1, but not Fus3. These findings reveal how feedback phosphorylation of a common pathway component can limit the activity of a competing MAP kinase through feedback phosphorylation of a common activator, and thereby promote signal fidelity