| The TOR signaling pathway regulates a wide scope of cellular activities, including the expression of genes involved in amino acid metabolism in budding yeast. This work focused on further characterizing the downstream pathways of TOR, as well as the interaction between TOR and other signaling pathways, specifically the PKA pathway.; One subset of TOR regulated genes is dependent on the RTG pathway, which was first identified as a mitochondria-to-nucleus signaling pathway required for production of alpha-ketoglutarate for use in glutamate and glutamine biosynthesis. Within the RTG pathway, the negative regulator Mks1p has also been identified as a negative regulator for lysine biosynthetic genes. It was further demonstrated that expression of lysine biosynthetic genes in mks1Delta cells requires the RTG pathway. In this work, a microarray analysis identified a concise set of genes derepressed in mks1Delta cells, which includes RTG target genes, lysine biosynthetic genes, and other uncharacterized genes. Functional partitioning of these uncharacterized genes identified one novel Rtg1p/Rtg3p target gene, PDH1, and two Lys14p targets, YJL200C and CTP1.; This work also characterized TOR as a positive regulator for lysine biosynthesis during lysine starvation conditions, which is independent of the RTG pathway. Instead, PKA is an important coregulator for this branch of the TOR pathway. Besides LYS genes, genes involved in branched chain amino acid biosynthesis and purine nucleotide biosynthesis are also positively regulated by TOR. The expression pattern of these genes is remarkably similar to ribosomal protein genes and genes involved in ribosomal biogenesis, but is distinct from other TOR/PKA coregulated genes, including genes involved in glucose fermentation and aerobic respiration. These results suggest that multiple modes of crosstalk might be involved in the coregulation between these two signaling pathways. Together, these results provide an example how multiple signaling pathways, general growth conditions, as well as the availability of specific nutrients contribute to the regulation of gene activity in yeast. |
