Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis

Time-dependent profiling of metabolites from Snf1 mutant and wild type yeast cells

The effect of sampling time in the context of growth conditions on a dynamic metabolic system was investigated in order to assess to what extent a single sampling time may be sufficient for general application, as well as to determine if useful kinetic information could be obtained. A wild type yeast strain (W) was compared to a snf1Delta mutant yeast strain (S) grown in high-glucose medium (R) and in low-glucose medium containing ethanol (DR). Under these growth conditions, different metabolic pathways for utilizing the different carbon sources are expected to be active. Thus, changes in metabolite levels relating to the carbon source in the growth medium were anticipated. Furthermore, the Snf1 protein kinase complex is required to adapt cellular metabolism from fermentative R conditions to oxidative DR conditions. So, differences in intracellular metabolite levels between the W and S yeast strains were also anticipated. Cell extracts were collected at four time points (0.5, 2, 4, 6 h) after shifting half of the cells from R to DR conditions, resulting in 16 sample classes (WR, WDR, SR, SDR) x (0.5, 2, 4, 6 h). The experimental design provided time course data, so temporal dependencies could be monitored in addition to carbon source and strain dependencies. Comprehensive two-dimensional (2D) gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-TOFMS) was used with discovery-based data mining algorithms ( Anal. Chem. 2006, 78, 5068-5075 (ref 1); J. Chromatogr., A 2008, 1186, 401-411 (ref 2)) to locate regions within the 2D chromatograms (i.e., metabolites) that provided chemical selectivity between the 16 sample classes. These regions were mathematically resolved using parallel factor analysis to positively identify the metabolites and to acquire quantitative results. With these tools, 51 unique metabolites were identified and quantified. Various time course patterns emerged from these data, and principal component analysis (PCA) was utilized as a comparison tool to determine the sources of variance between these 51 metabolites. The effect of sampling time was investigated with separate PCA analyses using various subsets of the data. PCA utilizing all of the time course data, averaged time course data, and each individual time point data set independently were performed to discern the differences. For the yeast strains examined in the current study, data collection at either 4 or 6 h provided information comparable to averaged time course data, albeit with a few metabolites missing using a single sampling time point.

Mathematical analysis of models for reaction kinetics in intracellular environments

Two models that have been proposed in the literature for description of kinetics in intracellular environments characterized by macromolecular crowding and inhomogeneities, are mathematically analyzed and discussed. The models are first derived by using phenomenological arguments that lead to generalizations of the law of mass action. The prediction of these models in the case of bimolecular binding reaction is then analyzed. It is mathematically proved that the models may predict qualitatively different behavior of progress curves. In particular, they also predict asymptotic steady state concentrations that cannot be reconciled. In this paper we propose and discuss generalizations of these models which under specified conditions lead to qualitatively similar behavior of reaction progress curves. We believe that these generalized models are better suited for data analysis.

A proteomic view of Candida albicans yeast cell metabolism in exponential and stationary growth phases

The facultative pathogenic fungus Candida albicans has to come up with dynamic metabolic adaptation programs in order to be able to survive within a variety of niches in the human host, each of which has its different nutrient availability. Using a large-scale two-dimensional (2-D) protein gel electrophoresis approach, we analyzed the adaptation mechanisms to nutrient limitation in a batch culture in complex medium with glucose as carbon source. To this end, we constructed a 2-D reference map of cytoplasmic proteins and quantitatively compared protein accumulation of growing yeast cells with those from the stationary phase. This yielded characteristic proteome signatures for each physiological state. During exponential growth, proteins required for the synthesis of RNA, DNA, and proteins, including components of purine and pyrimidine synthesis pathways and ribosomal proteins, were over-represented. The stationary-phase signature revealed a complex reprogramming of metabolic networks: Up-regulation of glyoxylate cycle, gluconeogenesis, and glutamate degradation signaled a switch to the utilization of alternative carbon sources instead of the exhausted glucose. Induction of proteins involved in defense against oxidative and heat stress indicates a change in redox balance and reactive oxygen species concentrations.

Phytoalexins and polar metabolites from the oilseeds canola and rapeseed: differential metabolic responses to the biotroph Albugo candida and to abiotic stress

The metabolites produced in leaves of the oilseeds canola and rapeseed (Brassica rapa L.) inoculated with either different races of the biotroph Albugo candida or sprayed with CuCl(2) were determined. This investigation established consistent phytoalexin (spirobrassinin, cyclobrassinin, and rutalexin) and phytoanticipin (indolyl-3-acetonitrile, arvelexin, caulilexin C, and 4-methoxyglucobrassicin) production in canola and rapeseed in response to both biotic and abiotic elicitation. In addition, a wide number of polar metabolites were isolated from infected leaves, including six new phenylpropanoids and two new flavonoids. The extractable chemical components of zoosporangia of A. candida and the anti-oomycete activity of phytoalexins were determined as well. Overall, the results suggest that during the initial stage of the interaction, leaves of B. rapa have a similar response to virulent and avirulent races of A. candida, with respect to the accumulation of chemical defenses. After this stage, despite the higher phytoalexin concentration, the "compatible" races could overcome the plant defense system for further infection, but growth of the "incompatible" races was inhibited. Since results of bioassays showed that cyclobrassinin and brassilexin were more inhibitory to A. candida than rutalexin, the apparent redirection of the phytoalexin pathway towards rutalexin, avoiding cyclobrassinin and brassilexin accumulation might be caused by the pathogen. Alternatively, A. candida might be able to detoxify both cyclobrassinin and brassilexin, similar to necrotrophic plant pathogens. Overall, the correlation between phytoalexin production in infected or stressed leaves and the outcome of the plant-pathogen interaction suggested that A. candida was able to elude the plant defense mechanisms by, for example, redirecting the phytoalexin biosynthetic pathway.

Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shift

BACKGROUND

The diauxic shift in yeast requires cells to coordinate a complicated response that involves numerous genes and metabolic processes. It is unknown whether responses of this type are mediated in vivo through changes in a few "key" genes and enzymes, which are mathematically characterized by high sensitivities, or whether they are based on many small changes in genes and enzymes that are not particularly sensitive. In contrast to global assessments of changes in gene or protein interaction networks, we study here control aspects of the diauxic shift by performing a detailed analysis of one specific pathway-sphingolipid metabolism-which is known to have signaling functions and is associated with a wide variety of stress responses.

RESULTS

The approach uses two components: publicly available sets of expression data of sphingolipid genes and a recently developed Generalized Mass Action (GMA) mathematical model of the sphingolipid pathway. In one line of exploration, we analyze the sensitivity of the model with respect to enzyme activities, and thus gene expression. Complementary to this approach, we convert the gene expression data into changes in enzyme activities and then predict metabolic consequences by means of the mathematical model. It was found that most of the sensitivities in the model are low in magnitude, but that some stand out as relatively high. This information was then deployed to test whether the cell uses a few of the very sensitive pathway steps to mount a response or whether the control is distributed throughout the pathway. Pilot experiments confirm qualitatively and in part quantitatively the predictions of a group of metabolite simulations.

CONCLUSION

The results indicate that yeast coordinates sphingolipid mediated changes during the diauxic shift through an array of small changes in many genes and enzymes, rather than relying on a strategy involving a few select genes with high sensitivity. This study also highlights a novel approach in coupling data mining with mathematical modeling in order to evaluate specific metabolic pathways.

Tps1 regulates the pentose phosphate pathway, nitrogen metabolism and fungal virulence

Trehalose fulfils a wide variety of functions in cells, acting as a stress protectant, storage carbohydrate and compatible solute. Recent evidence, however, indicates that trehalose metabolism may exert important regulatory roles in the development of multicellular eukaryotes. Here, we show that in the plant pathogenic fungus Magnaporthe grisea trehalose-6-phosphate (T6P) synthase (Tps1) is responsible for regulating the pentose phosphate pathway, intracellular levels of NADPH and fungal virulence. Tps1 integrates glucose-6-phosphate (G6P) metabolism with nitrogen source utilisation, and thereby regulates the activity of nitrate reductase. Activity of Tps1 requires an associated regulator protein Tps3, which is also necessary for pathogenicity. Tps1 controls expression of the nitrogen metabolite repressor gene, NMR1, and is required for expression of virulence-associated genes. Functional analysis of Tps1 indicates that its regulatory functions are associated with binding of G6P, but independent of Tps1 catalytic activity. Taken together, these results demonstrate that Tps1 is a central regulator for integration of carbon and nitrogen metabolism, and plays a pivotal role in the establishment of plant disease.

On the robust circuit design schemes of biochemical networks: steady-state approach

Based on the steady-state analyses of the synergism and saturation system (S-system) model, a robust control method is proposed for biochemical networks via feedback and feedforward biochemical circuits. Two robust biochemical circuit design schemes are developed. One scheme is to improve the system's structural stability so as to tolerate larger kinetic parameter variations, whereas the other is to compensate for the kinetic parameter variations to eliminate their effects. In addition, a multi-objective biochemical circuit design scheme is introduced for both the robust design against kinetic parameter variations and a desired sensitivity design to eliminate the effect of external disturbance simultaneously. The proposed robust circuit design schemes will provide a systematic method with potential applications in synthetic circuit design for biotechnological purpose and drug design purpose. Recent advances in both metabolic and genetic engineering have made the robust biochemical circuit control approach feasible through the design and implementation of synthetic biological networks amenable to mathematical modeling and quantitative analysis. Finally, several examples including the robust circuit design of the tricarboxylic acid cycle are used in silico to illustrate the design procedure and to confirm the performance of the proposed design method.

Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry analysis of metabolites in fermenting and respiring yeast cells

Comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry coupled with rapid chemometric analysis were used to identify chemical differences in metabolite extracts isolated from yeast cells either metabolizing glucose (repressed (R) cells) via fermentation or metabolizing ethanol by respiration (derepressed (DR) cells). Principal component analysis (PCA) followed by parallel factor analysis (PARAFAC) in concert with the LECO ChromaTOF software located and identified the differences in composition between the two types of cell extracts and provided a reliable ratio of the metabolite concentrations. In this report, we demonstrate the analytical method developed to provide relatively rapid analysis of three selective mass channels (m/z 73, 205, 387), although in principle all collected mass channels could be analyzed. Twenty-six metabolites that differentiate repressed cells from derepressed cells were identified. The DR/R ratio of metabolite concentrations ranged from 0.02 for glucose to 67 for trehalose. The average biological variation of the sample extracts was 31%. This analysis demonstrates the utility and benefit of using PCA combined with PARAFAC and ChromaTOF software on extremely complex samples to derive useful information from complex three-dimensional chromatographic data objectively and relatively rapidly.

Trehalose synthesis in Saccharomycopsis fibuligera does not respond to stress treatments

Synthesis of trehalose in Saccharomycopsis fibuligera sdu under various stress conditions was investigated. Neither the activation of trehalose-6-phosphate synthase (SfTPS1) nor the change in trehalose content was observed under stress exposure of S. fibuligera sdu cells. The results of reverse transcription polymerase chain reaction, which was performed with the specific primers designed to target the SfTPS1 gene fragment cloned from this strain, also showed that all stress treatments did not increase the expression of SfTPS1 gene. These results demonstrated that synthesis of trehalose in response to stress conditions in S. fibuligera sdu clearly differs from that of Saccharomyces cerevisiae and most other fungi. The phylogenetic analysis of the amino acid sequence deduced from the SfTPS1 gene fragment showed that the SfTPS1 sequence formed a separate family that was far related to S. cerevisiae TPS1. The yeast strain, which can accumulate a large amount of trehalose under normal growth conditions, has many applications and TPS1 gene in such strain may have unique use in transgenic organisms.

Isoforms of trehalase and invertase of Fusarium oxysporum

Enzymatic assays and native PAGE were used to study trehalase and invertase activities, depending on culture age and different sugar conditions, in cell-free extracts, culture filtrates and ribosomal wash of Fusarium oxysporum. The activity of invertase preceded that of trehalase; in the exponential phase of growth, mainly invertase activity was produced, whereas trehalase activity was high in the stationary phase. In this last phase of growth, the activity of intracellular trehalase was repressed by monosaccharides, whereas disaccharides, especially lactose and starch, enhanced the activity of intracellular and extracellular trehalase. However, invertase activity was not repressed under these conditions and had the maximal activity in the presence of saccharose. Intracellular trehalase appeared in a single, high-molecular weight (120 kDa) form, whereas the extracellular enzyme appeared in a single, low-molecular weight (60 kDa) form. The activity pattern of invertase isoforms indicated the occurrence of three forms of intracellular enzyme with the main activity band at 120 kDa and two isoforms of extracellular enzyme. In the ribosomal wash, high-molecular weight isoforms of both trehalase and invertase were identified. A possible role of trehalase and invertase in carbohydrate metabolism of fungal pathogens is also discussed.

Trehalose accumulation in a high-trehalose-accumulating mutant of Saccharomycopsis fibuligera sdu does not respond to stress treatments

The isolation of high-trehalose-accumulating mutant A11 from Saccharomycopsis fibuligera sdu has been previously described. In this paper, accumulation of trehalose under various stress conditions in S. fibuligera A11 was investigated. Neither activation of trehalose-6-phosphate synthase (SfTps1) nor change in trehalose content was observed under stress exposure of S. fibuligera A11 cells. A fragment of the Sftps1 gene in this strain was also cloned by degenerate PCR using the CoDeHOP strategy and multiply-aligned Tps1 sequences. This sequence allowed us to investigate the expression of the Sftps1 gene, which was also kept constant under the various stress conditions. Altogether, these results indicate that trehalose metabolism in S. fibuligera A11 in response to stress conditions clearly differs from that of Saccharomyces cerevisiae and most other fungi. The expression of the Sftps1 gene was not responsive to different stress treatments.

Trehalose turnover during abiotic stress in arbuscular mycorrhizal fungi

Trehalose is a common reserve carbohydrate in fungi, whose role has been recently extended to other cellular functions, such as stress tolerance, glycolysis control, sporulation and infectivity of some pathogenic strains. To gain some insight into the role of trehalose during abiotic stress in arbuscular mycorrhizal (AM) fungi, we assessed trehalose content as well as transcriptional regulation and enzyme activity of neutral trehalase and trehalose-6-phosphate phosphatase in Glomus intraradices in response to heat shock, chemical or osmotic stress. Prolonged or intensive exposure to heat or chemical stress, but not osmotic stress, caused an increase of trehalose in the cell. We found this associated with transient up-regulation of the trehalose-6-P phosphatase (GiTPS2) transcript that coincided with moderate increases in enzyme activity. By contrast, there were no changes in neutral trehalase (GiNTH1) RNA accumulation in response to stress treatments, while they promoted, in most cases, an increase in activity. After stress had ceased, trehalose returned to basal concentrations, pointing to a role of neutral trehalase activity in heat shock recovery. A yeast complementation assay confirmed the role of neutral trehalase in thermotolerance. Taken together, these results indicate that trehalose could play a role in AM fungi during the recovery from certain stresses such as heat shock and chemical treatment.

Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations

Cooperative and saturable systems are common in molecular biology. Nevertheless, common canonical formalisms for kinetic modeling that are theoretically well justified do not have a saturable form. Modeling and fitting data from saturable systems are widely done using Hill-like equations. In practice, there is no theoretical justification for the generalized use of these equations, other than their ability to fit experimental data. Thus it is important to find a canonical formalism that is (a) theoretically well supported, (b) has a saturable functional form, and (c) can be justifiably applicable to any biochemical network. Here we derive such a formalism using Taylor approximations in a special transformation space defined by power-inverses and logarithms of power-inverses. This formalism is generalized for processes with n-variables, leading to a useful mathematical representation for molecular biology: the Saturable and Cooperative Formalism (SC formalism). This formalism provides an appropriate representation that can be used for modeling processes with cooperativity and saturation. We also show that the Hill equation can be seen as a special case within this formalism. Parameter estimation for the SC formalism requires information that is also necessary to build Power-Law models, Metabolic Control Analysis descriptions or (log)linear and Lin-log models. In addition, the saturation fraction of the relevant processes at the operating point needs to be considered. The practical use of the SC formalism for modeling is illustrated with a few examples. Similar models are built using different formalisms and compared to emphasize advantages and limitations of the different approaches.

Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock

Background

Understanding the relationship between gene expression changes, enzyme activity shifts, and the corresponding physiological adaptive response of organisms to environmental cues is crucial in explaining how cells cope with stress. For example, adaptation of yeast to heat shock involves a characteristic profile of changes to the expression levels of genes coding for enzymes of the glycolytic pathway and some of its branches. The experimental determination of changes in gene expression profiles provides a descriptive picture of the adaptive response to stress. However, it does not explain why a particular profile is selected for any given response.

Results

We used mathematical models and analysis of in silico gene expression profiles (GEPs) to understand how changes in gene expression correlate to an efficient response of yeast cells to heat shock. An exhaustive set of GEPs, matched with the corresponding set of enzyme activities, was simulated and analyzed. The effectiveness of each profile in the response to heat shock was evaluated according to relevant physiological and functional criteria. The small subset of GEPs that lead to effective physiological responses after heat shock was identified as the result of the tuning of several evolutionary criteria. The experimentally observed transcriptional changes in response to heat shock belong to this set and can be explained by quantitative design principles at the physiological level that ultimately constrain changes in gene expression.

Conclusion

Our theoretical approach suggests a method for understanding the combined effect of changes in the expression of multiple genes on the activity of metabolic pathways, and consequently on the adaptation of cellular metabolism to heat shock. This method identifies quantitative design principles that facilitate understating the response of the cell to stress.

Fungal heat-shock proteins in human disease

Heat-shock proteins (hsps) have been identified as molecular chaperones conserved between microbes and man and grouped by their molecular mass and high degree of amino acid homology. This article reviews the major hsps of Saccharomyces cerevisiae, their interactions with trehalose, the effect of fermentation and the role of the heat-shock factor. Information derived from this model, as well as from Neurospora crassa and Achlya ambisexualis, helps in understanding the importance of hsps in the pathogenic fungi, Candida albicans, Cryptococcus neoformans, Aspergillus spp., Histoplasma capsulatum, Paracoccidioides brasiliensis, Trichophyton rubrum, Phycomyces blakesleeanus, Fusarium oxysporum, Coccidioides immitis and Pneumocystis jiroveci. This has been matched with proteomic and genomic information examining hsp expression in response to noxious stimuli. Fungal hsp90 has been identified as a target for immunotherapy by a genetically recombinant antibody. The concept of combining this antibody fragment with an antifungal drug for treating life-threatening fungal infection and the potential interactions with human and microbial hsp90 and nitric oxide is discussed.

Both heat-shock and cold-shock influence trehalose metabolism in an entomopathogenic nematode

Heat-shock response is highly conserved in animals and microorganisms, and it results in the synthesis of heat-shock proteins. In yeast, heat-shock response has also been reported to induce trehalose accumulation. We explored the relationship between heat- (35 C) or cold-shock (1 and 10 C) and trehalose metabolism in the entomopathogenic nematode, Heterorhabditis bacteriophora. Because both heat- and cold-shocks may precede desiccation stress in natural soil environments, we hypothesized that nematodes may accumulate a general desiccation protectant, trehalose, under both situations. Indeed, both heat- and cold-shocks influenced trehalose accumulation and activities of enzymes of trehalose metabolism in H. bacteriophora. Trehalose increased by 5- and 6-fold in heat- and cold-shocked infective juveniles, respectively, within 3 hr of exposure, compared with the nematodes maintained at 25 C (culture temperature). The activity of trehalose-6-phosphate synthase (T6PS), an enzyme involved in the synthesis of trehalose, also significantly increased in both heat- and cold-shocked nematodes during the first 3 hr of exposure. Generally, the trehalose levels and activities of T6PS declined to their original levels within 3 hr when nematodes were transferred back to 25 C. In both heat- and cold-shocked nematodes, trehalase activity decreased significantly within the first 3 hr and generally returned to the original levels within 3 hr when these nematodes were transferred back to 25 C. The results demonstrate that the trehalose concentrations in H. bacteriophora are influenced by both heat- and cold-shocks and are regulated by the action of 2 trehalose-metabolizing enzymes, T6PS and trehalase. The accumulated trehalose may enhance survival of nematodes under both cold and warm conditions, but it may also provide simultaneous protection against desiccation that may result from subsequent evaporation or freezing. This is the first report of the relationship between trehalose metabolism and heat-shock for the Nematoda.

Extracellular trehalose utilization by Saccharomyces cerevisiae

Two haploid strains of Saccharomyces cerevisiae viz. MATalpha and MATa were grown in glucose and trehalose medium and growth patterns were compared. Both strains show similar growth, except for an extended lag phase in trehalose grown cells. In both trehalose grown strains increase in activities of both extracellular trehalase activities and simultaneous decrease in extracellular trehalose level was seen. This coincided with a sharp increase in extracellular glucose level and beginning of log phase of growth. Alcohol production was also observed. Secreted trehalase activity was detected, in addition to periplasmic activity. It appeared that extracellular trehalose was hydrolyzed into glucose by extracellular trehalase activity. This glucose was utilized by the cells for growth. The alcohol formation was due to the fermentation of glucose. Addition of extracellular trehalase caused reduction in the lag phase when grown in trehalose medium, supporting our hypothesis of extracellular utilization of trehalose.

Overview and perspectives on the transcriptome of Paracoccidioides brasiliensis

Paracoccidioides brasiliensis is a dimorphic and thermo-regulated fungus which is the causative agent of paracoccidioidomycosis, an endemic disease widespread in Latin America that affects 10 million individuals. Pathogenicity is assumed to be a consequence of the dimorphic transition from mycelium to yeast cells during human infection. This review shows the results of the P. brasiliensis transcriptome project which generated 6,022 assembled groups from mycelium and yeast phases. Computer analysis using the tools of bioinformatics revealed several aspects from the transcriptome of this pathogen such as: general and differential metabolism in mycelium and yeast cells; cell cycle, DNA replication, repair and recombination; RNA biogenesis apparatus; translation and protein fate machineries; cell wall; hydrolytic enzymes; proteases; GPI-anchored proteins; molecular chaperones; insights into drug resistance and transporters; oxidative stress response and virulence. The present analysis has provided a more comprehensive view of some specific features considered relevant for the understanding of basic and applied knowledge of P. brasiliensis.

Controllability of non-linear biochemical systems

Mathematical methods of biochemical pathway analysis are rapidly maturing to a point where it is possible to provide objective rationale for the natural design of metabolic systems and where it is becoming feasible to manipulate these systems based on model predictions, for instance, with the goal of optimizing the yield of a desired microbial product. So far, theory-based metabolic optimization techniques have mostly been applied to steady-state conditions or the minimization of transition time, using either linear stoichiometric models or fully kinetic models within biochemical systems theory (BST). This article addresses the related problem of controllability, where the task is to steer a non-linear biochemical system, within a given time period, from an initial state to some target state, which may or may not be a steady state. For this purpose, BST models in S-system form are transformed into affine non-linear control systems, which are subjected to an exact feedback linearization that permits controllability through independent variables. The method is exemplified with a small glycolytic-glycogenolytic pathway that had been analyzed previously by several other authors in different contexts.

Yeast sphingolipid metabolism: clues and connections

This review of sphingolipid metabolism in the budding yeast Saccharomyces cerevisiae contains information on the enzymes and the genes that encode them, as well as connections to other metabolic pathways. Particular attention is given to yeast homologs, domains, and motifs in the sequence, cellular localization of enzymes, and possible protein-protein interactions. Also included are genetic interactions of special interest that provide clues to the cellular biological roles of particular sphingolipid metabolic pathways and specific sphingolipids.

Identification of new genes regulated by the Crt1 transcription factor, an effector of the DNA damage checkpoint pathway in Saccharomyces cerevisiae

The Crt1 (RFX1) protein in Saccharomyces cerevisiae is an effector of the DNA damage checkpoint pathway. It recognizes a 13-bp cis-regulatory element in the 5'-untranslated region (5'-UTR) of the ribonucleotide reductase genes RNR2, RNR3, and RNR4; the HUG1 gene; and itself. We calculated the weight matrix representing the Crt1p binding site motif according to analysis of the 5'-UTR sequences of the genes that are under its regulation. We subsequently searched the 5'-UTR sequences of all the genes in the yeast genome for the occurrence of this motif. The motif was found in regulatory regions of 30 genes. A statistical analysis showed that it is unlikely that a random gene cluster contains the motif conserved as well as the Crt1p binding site. Analysis of microarray data provided supporting evidence for five putative Crt1p targets: FSH3, YLR345W, UBC5, NDE2, and NTH2. We used reverse transcription-PCR to compare the expression levels of these genes in wild-type and crt1Delta strains. Our results indicated that FSH3, YLR345W, and NTH2 are indeed under the regulation of Crt1p. Sequence analysis of the FSH3p indicated that this protein may be involved in folate metabolism either by carrying serine hydrolase activity required for the novel metabolic pathway involving dihydrofolate reductase (DHFR) or by directly interacting with the DHFR enzyme. We postulate that Crt1p may influence deoxyribonucleotide synthesis not only by regulating expression of the RNR genes but also by modulating DHFR activity. FSH3p shares significant sequence similarity with the product of the human tumor suppressor gene OVCA2. YLR345Wp and NTH2p are enzymes involved in the central metabolism under stress conditions.

Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models

For the first time, kinetic information from the literature was collected and used to construct integrative dynamical mathematical models of sphingolipid metabolism. One model was designed primarily with kinetic equations in the tradition of Michaelis and Menten whereas the other two models were designed as alternative power-law models within the framework of Biochemical Systems Theory. Each model contains about 50 variables, about a quarter of which are dependent (state) variables, while the others are independent inputs and enzyme activities that are considered constant. The models account for known regulatory signals that exert control over the pathway. Standard mathematical testing, repeated revisiting of the literature, and numerous rounds of amendments and refinements resulted in models that are stable and rather insensitive to perturbations in inputs or parameter values. The models also appear to be compatible with the modest amount of experimental experience that lends itself to direct comparisons. Even though the three models are based on different mathematical representations, they show dynamic responses to a variety of perturbations and changes in conditions that are essentially equivalent for small perturbations and similar for large perturbations. The kinetic information used for model construction and the models themselves can serve as a starting point for future analyses and refinements.