Table I. Genome-wide effects of glutamate on gene expression.
| Gene expression | ORF | Gene | Gene product/function | Fold change |
|---|---|---|---|---|
| Repressed NCR target genes | ||||
| YNL142W | MEP2 | ammonia permease of low capacity and high affinity | 14.3 | |
| YKR039W | GAP1 | general amino acid permease | 14.0 | |
| YKR034W | DAL80 | negative regulator of multiple nitrogen catabolic genes | 12.4 | |
| YLR158C | ASP3C | l-asparaginase II, extracellular | 9.0 | |
| YIR032C | DAL3 | ureidoglycolate hydrolase | 7.7 | |
| YLR155C | ASP3A | l-asparaginase II, extracellular | 7.5 | |
| YLR157C | ASP3B | l-asparaginase II, extracellular | 7.4 | |
| YLR160C | ASP3D | l-asparaginase II, extracellular | 5.8 | |
| YJR152W | DAL5 | allantoate permease | 5.1 | |
| YIR031C | DAL7 | malate synthase 2 | 4.5 | |
| YLR142W | PUT1 | proline oxidase | 3.3 | |
| YOR348C | PUT4 | putative proline-specific permease | 2.7 | |
| RTG target genes | ||||
| YLR304C | ACO1 | aconitase, mitochondrial | 6.5 | |
| YCR005C | CIT2 | non-mitochondrial citrate synthase | 3.3 | |
| YOR136W | IDH2 | NAD+-dependent isocitrate dehydrogenase | 3.1 | |
| Others | ||||
| YKR033C | protein of unknown function | 11.4 | ||
| YLR348C | DIC1 | mitochondrial dicarboxylate transport protein | 5.4 | |
| YLR349W | protein of unknown function | 4.4 | ||
| YBR182C | SMP1 | probable transcription factor | 4.3 | |
| YBR294W | SUL1 | probable sulfate transport protein | 4.2 | |
| YPL058C | PDR12 | multidrug resistance transporter | 3.6 | |
| YNL208W | protein of unknown function | 3.2 | ||
| YOR135C | protein of unknown function | 2.9 | ||
| YJL172W | CPS1 | carboxypeptidase yscS | 2.9 | |
| YGL045W | protein of unknown function | 2.7 | ||
| YML131W | putative NAD-dependent oxidoreductase | 2.7 | ||
| YLR161W | protein of unknown function | 2.7 | ||
| YER124C | protein of unknown function | 2.6 | ||
| YLL053C | aquaporin water channel protein | 2.6 | ||
| YIL121W | member of MFS-MDR family of multidrug permeases | 2.5 | ||
| YGL028C | SCW11 | soluble cell wall protein | 2.5 | |
| Induced | ||||
| Amino acid permeases | ||||
| YDR046C | BAP3 | valine transporter | 22.9 | |
| YDR068 | BAP2 | probable amino acid permease for leucine, isoleucine and valine | ||
| YDR | 20.0 | |||
| YCL025C | AGP1 | amino acid permease | 12.1 | |
| YBR069C | VAP1 | probable amino acid transport protein | 12.0 | |
| YDR508C | GNP1 | high-affinity glutamine permease | 6.1 | |
| YGR055W | MUP1 | high-affinity methionine permease | 4.3 | |
| Proteases | ||||
| YIR039C | YPS6 | GPI-anchored aspartic protease | 6.6 | |
| YOL154W | protein with similarity to zinc metalloproteinases | 2.8 | ||
| Other | ||||
| YDR509W | protein of unknown function | 4.8 | ||
| YNL160W | YGP1 | glycoprotein synthesized in response to nutrient limitation | 3.8 | |
| YMR011W | HXT2 | high-affinity hexose transporter-2 | 3.6 | |
| YBR092C | PHO3 | acid phosphatase, constitutive | 3.2 | |
| YOL158C | ENB1 | enterobactin transporter | 3.0 | |
| YNL065W | member of MFS-MDR family of multidrug permeases | 2.7 |
Four independent cultures of strain S288C were grown to mid-log phase in YNB5%D with or without 0.2% glutamate. After isolation of poly(A)+ RNA from each, labeled cDNAs were made with either Cy3 or Cy5 and mixed with the oppositely labeled cDNA from treated or untreated samples. The indicated fold changes in gene expression were determined as described in Epstein et al. (2001a) using a cut-off of 2.5-fold change in the average of the expression ratios from two independent RNA preparations, each repeated with reversal of Cy3 and Cy5 labeling.