Two forms of serine transhydroxymethylase, one absent in a thymidylate-less mutant in Saccharomyces cerevisiae

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.

Characterization of genes that are synthetically lethal with ade3 or leu2 in Saccharomyces cerevisiae

Combinations of two non-lethal mutations that result in cell death are synthetically lethal. Such a genetic relationship suggests a functional interaction between the corresponding gene products. Frequently, an ade2 ade3 colony-sectoring assay is used to screen for synthetic lethal mutants. In these screens, mutants are sought that fail to lose a plasmid that bears a gene of interest. However, a subset of mutants is often found that is dependent on plasmid components other than the target gene. To understand the mechanism of this dependence, we characterized those mutants that, although prevalent in most mutant hunts, are usually discarded. Using a LEU2-ADE3 plasmid, plasmid-dependent mutations were found in the SHM2, PTR3, BAP2 and SSY1 genes. Double shm2 ade3 mutants are non-viable because the two pathways for tetrahydrofolate synthesis are blocked. Mutations in PTR3, BAP2 and SSY1 disrupt sensing and transport of extracellular leucine. Therefore, ptr3, bap2 or ssy1 mutants must be leucine prototrophs to grow on rich media. In light of these findings, we propose modifications that should improve the efficiency of synthetic lethal screening procedures.

Purification and partial characterization of three isoforms of serine hydroxymethyltransferase from Crithidia fasciculata

Three molecular forms of serine hydroxymethyltransferase (SHMT) have been detected in choanomastigotes of Crithidia fasciculata by DEAE-cellulose chromatography. The three isoforms (named SHMT I, II, and III) presented small differences in charge and molecular weight. Digitonin treatment of intact cells suggested that SHMT III is cytosolic, whereas the other two isoforms are particle bound, one being mitochondrial (SHMT I) and the other one very likely glycosomal (SHMT II). The three SHMT isoforms were purified to homogeneity, and their physicochemical and kinetic properties studied. Determination of their native and subunit molecular masses revealed that all of them have a tetrameric structure. The three isoforms were shown to be PLP-dependent enzymes after L-cysteine and hydroxylamine hydrochloride treatments. They showed similar pH optima, bimodal kinetics for L-serine and Michaelis-Menten kinetics for THF.

The phenotype of a dihydrofolate reductase mutant of Saccharomyces cerevisiae

We have constructed a dihydrofolate reductase mutant (dfr1) of Saccharomyces cerevisiae. The mutant has auxotrophic growth requirements for the C1 metabolites dTMP, adenine, histidine and methionine, similar to those of wild-type (wt) strains grown in the presence of methotrexate (MTX). However, unlike wt strains treated with MTX, the growth requirements of the dfr1 mutant are not satisfied by exogenous 5-formyltetrahydrofolic acid (FA; folinic acid) in complex (YEPD) medium. This result is surprising, as yeast cells treated with MTX are expected to be phenocopies of dfr1 mutants. The inability of the mutants to metabolize FA suggests that the DFR1 gene product may have a role in folate metabolism in addition to its well-characterized function in the reduction of dihydrofolate. From dfr1 strains, we have isolated secondary mutants whose growth can be supported by FA in YEPD medium. This FA-utilizing phenotype is attributable to recessive mutations which we have designated fou. In addition to their inability to metabolize FA, the dfr1 strains are unable to grow on medium containing the non-fermentable carbon source glycerol, suggesting that the DFR1 gene product is also required for mitochondrial function. In order to overcome this lack of respiratory activity in the dfr1 mutants, we isolated strains containing a dominant mutation, DIR, which allows growth on glycerol in the presence of antifolate drugs. When crossed into dfr1 strains, the DIR mutation conferred respiratory competence. These strains should be useful in a variety of studies on the genetics and biochemistry of folate metabolism in this simple eukaryote.

Molecular characterization of the Saccharomyces cerevisiae dihydrofolate reductase gene (DFR1)

The complete nucleotide sequence of a 1957 bp DNA fragment containing the dihydrofolate reductase gene (DFR1) of the yeast Saccharomyces cerevisiae is presented. Within this region a single open reading frame of 633 base pairs was found which is capable of encoding a 211 amino acid residue protein with a calculated Mr of 24,233. The amino acid sequence derived from the yeast DFR1 gene shows limited homology with sequences from both eukaryotic and non-eukaryotic DHFR enzymes. Northern blot hybridization reveals that the mRNA from this gene is a 900 base polyadenylated transcript. Yeast strains containing the cloned DFR1 gene on multicopy number shuttle vector plasmids show dramatically enhanced methotrexate resistance. Consensus DNA sequences responsible for RNA polymerase II interaction and general amino acid control in S. cerevisiae are located within the 5'-noncoding region with respect to the open reading frame. The DNA fragment containing these sequences has been shown to be necessary for DFR1 gene expression in both S. cerevisiae and E. coli.

Isolation and characterization of yeast mutants auxotrophic for 2'-deoxythymidine 5'-monophosphate

Mutant strains of Saccharomyces cerevisiae auxotrophic for deoxythymidine monophosphate (dTMP) were isolated and characterized. Two distinct classes of auxotrophs were obtained. One class had a simple requirement for dTMP and was analogous to thymine-requiring bacteria. The second class required dTMP, adenine, histidine and methionine and this complex nutritional phenotype was due to defects in folate metabolism. The dTMP-dependent growth of respiratory-competent grande auxotrophs was found to be markedly affected by media composition and carbon source. In the absence of dTMP thymineless death occurred in both mutant classes.