Nitrogen catabolite repression in Saccharomyces cerevisiae

In Saccharomyces cerevisiae the expression of all known nitrogen catabolite pathways are regulated by four regulators known as Gln3, Gat1, Dal80, and Deh1. This is known as nitrogen catabolite repression (NCR). They bind to motifs in the promoter region to the consensus sequence 5′ GATAA 3′. Gln3 and Gat1 act positively on gene expression whereas Dal80 and Deh1 act negatively. Expression of nitrogen catabolite pathway genes known to be regulated by these four regulators are glutamine, glutamate, proline, urea, arginine, GABA, and allantoine. In addition, the expression of the genes encoding the general amino acid permease and the ammonium permease are also regulated by these four regulatory proteins. Another group of genes whose expression is also regulated by Gln3, Gat1, Dal80, and Deh1 are some protease, CPS1, PRB1, LAP1, and PEP4, responsible for the degradation of proteins into amino acids thereby providing a nitrogen source to the cell. In this review, all known promoter sequences related to expression of nitrogen catabolite pathways are discussed as well as other regulatory proteins. Overview of metabolic pathways and promotors are presented.     

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

Nutrient sensing and coordination of metabolic pathways are crucial functions for all living cells, but details of the coordination under different environmental conditions remain elusive. We therefore undertook a systems biology approach to investigate the interactions between the Snf1 and the target of rapamycin complex 1 (TORC1) in Saccharomyces cerevisiae. We show that Snf1 regulates a much broader range of biological processes compared with TORC1 under both glucose‐ and ammonium‐limited conditions. We also find that Snf1 has a role in upregulating the NADP⁺‐dependent glutamate dehydrogenase (encoded by GDH3) under derepressing condition, and therefore may also have a role in ammonium assimilation and amino‐acid biosynthesis, which can be considered as a convergence of Snf1 and TORC1 pathways. In addition to the accepted role of Snf1 in regulating fatty acid (FA) metabolism, we show that TORC1 also regulates FA metabolism, likely through modulating the peroxisome and β‐oxidation. Finally, we conclude that direct interactions between Snf1 and TORC1 pathways are unlikely under nutrient‐limited conditions and propose that TORC1 is repressed in a manner that is independent of Snf1.     

Deletion of OSH3 gene confers resistance against ISP-1 in Saccharomyces cerevisiae

Sphingolipids have been reported to regulate the growth and death of mammalian and yeast cells, but their precise mechanisms are unknown. In this paper, it was shown that the deletion of the oxysterol binding protein homologue 3 (OSH3) gene confers hyper resistance against ISP-1, an inhibitor of sphingolipid biosynthesis, in the yeast Saccharomyces cerevisiae. Furthermore, the overexpression of the ROK1 gene, which directly binds to Osh3p, conferred resistance against ISP-1, and the deletion of the KEM1 gene, which regulates microtubule functions, exhibited ISP-1 hypersensitivity. And yet, an ISP-1 treatment caused an abnormal mitotic spindle formation, and the ISP-1-induced cell cycle arrest was rescued by the deletion of the OSH3 gene. Taken together, it is suggested that the expression levels of the OSH3 gene influence the ISP-1 sensitivity of S. cerevisiae, and the sphingolipids are necessary for normal mitotic spindle formation in which the Osh3p may play a pivotal role.     

Characterization of IKI1 and IKI3 Genes Conferring pGKL Killer Sensitivity on Saccharomyces cerevisiae

The Saccharomyces cerevisiae iki mutants show an insensitive phenotype to the pGKL killer toxin, and we have cloned some IKI genes by complementation of this phenotype [Kishida et al., Biosci. Biotech. Biochem., 60, 798–801 (1996)]. Here, we identified and characterized the IKI1 and IKI3 genes. DNA sequencing of the genes showed that both have 100% identity with hypothetical genes identified by the yeast genome project, YHR187w (481,911–480,985 in chromosome VIII) for IKI1, and YLR384c (888,852–892,898 in chromosome XII) for IKI3. Both are novel genes with no significant identity with other known genes and they do not belong to any homology domain group, gene family, or superfamily. The disruption of IKI1 is not lethal, but growth of the disruptant was slower than that of the wild type at all temperatures examined. The disruptant was the killer-insensitive phenotype. The sequence of the IK11 gene predicted a hydrophilic protein with a molecular mass of 35 kDa (309 amino acids). A 35-kDa protein band was also detected by immunoblotting the 25,000 × g pellet fraction of the wild type yeast cell lysate. Disruption of the IKI3 gene is also non-lethal and it has the killer-insensitive phenotype. Iki3p may contain a transmembrane domain near the NH₂-terminal region (97–113 residues in a total of 1349 amino acids).