Table 2.
Summary of Nitrogen-regulated Genes Identified by Microarray Analysis
| Functional class | ORF | Gene | Description | Expression ratio* | |
|---|---|---|---|---|---|
| Genes preferentially expressed in glutamine | |||||
| Transporters | YDR046C | BAP3 | Amino acid permease | 12.5 | |
| YBR068C | BAP2 | Amino acid permease | 17.4 | ||
| YCL025C | AGP1 | Amino acid permease | 12.3 | ||
| YBR069C | VAP1 | Amino acid permease | 3.5 | ||
| YOL020W | TAT2 | Tryptophan permease | 3.4 | ||
| YDR508C | GNP1 | Glutamine permease | 3.1 | ||
| YGR055W | MUP1 | Methionine permease | 10.6 | ||
| YER064C | Unknown | Putative small molecule transporter | 3.3 | ||
| YNL065W | Unknown | Putative small molecule transporter | 3.2 | ||
| Miscellaneous | YNL160W | YGP1 | Stationary phase secreted glycoprotein | 9.4 | |
| YCR021C | HSP30 | Plasma membrane heat shock protein | 4.6 | ||
| YFL014W | HSP12 | Glucose and lipid heat shock protein | 3.8 | ||
| Genes preferentially expressed in urea | |||||
| DAL cluster group | YIR027C | DAL1 | Allantoinase | 14.2 | |
| YIR029W | DAL2 | Allantoinase | 12.7 | ||
| YIR032C | DAL3 | Ureidoglycolate hydrolase | 5.3 | ||
| YIR028W | DAL4 | Allantoin permease | 18.8 | ||
| YJR152W | DAL5 | Allantoate and ureidosuccinate permease | 17.8 | ||
| YIR031C | DAL7 | Glyoxysomal malate synthase | 34.4 | ||
| YKR034W | DAL80 | Repressor of GLN3 function | 4.3 | ||
| Transporters | YKR039W | GAP1 | General amino acid permease | 5.3 | |
| YNL142W | MEP2 | Ammonia permease | 17.3 | ||
| YBR294W | SUL1 | Sulfate transport protein | 4.2 | ||
| YHL016C | DUR3 | Urea permease | 35.9 | ||
| YLR348C | DIC1 | Mitochondrial dicarboxylate carrier | 3.3 | ||
| YPL265W | DIP5 | Dicaroboxylic amino acid permease | 7.5 | ||
| Metabolism/Enzymes | YBR208C | DUR1,2 | Urea amidolyase | 5.4 | |
| YLR142W | PUT1 | Proline oxidase | 10.6 | ||
| YPR035W | GLN1 | Glutamine synthetase | 6.9 | ||
| YNL117W | MLS1 | Malate synthase 1 | 4.8 | ||
| YGL062W | PYC1 | Pyruvate carboxylase 1 | 7.5 | ||
| YLR304C | ACO1 | Aconitate hydratase | 9.5 | ||
| YNL037C | IDH1 | Isocitrate dehydrogenase 1 | 7.7 | ||
| YOR136W | IDH2 | Isocitrate dehydrogenase 2 | 8.4 | ||
| YCR005C | CIT2 | Peroxisomal citrate synthase | 10.5 | ||
| YEL071W | DLD3 | d-Lactate dehydrogenase 3 | 9.1 | ||
Prototrophic strain S288c was grown to 0.5 OD600/ml in 1 liter minimal dextrose media containing 0.2% glutamine or 0.2% urea as sole nitrogen sources. PolyA mRNA was isolated and used to prepare cDNAs that were fluorescently labeled with either Cy3 or Cy5 fluorescent dyes. Samples were mixed and applied to DNA microarrays containing .6,200 individual yeast genes and analyzed using a microarray laser reader. Shown are the results of three independent experiments. In two of these experiments, each sample was labeled with Cy3 as well as Cy5, generating a total of five independent microarrays used for analysis. Listed genes displayed a mean difference ratio of 3.0 or greater in each of the five microarrays. Several genes known from previous studies to be regulated by glutamine did not meet these strict criteria, including PUT4, ARG3, CAR1, and ASP3,4. Thus, this list is likely to represent an underestimate of the total number of glutamine-regulated genes. Gene names and descriptions were obtained from the SGD (http://genome-www.stanford.edu/Saccharomyces) and YPD (http://www.proteome.com/databases/index) databases. *Genes preferentially expressed in glutamine (glutamine vs. urea), genes preferentially expressed in urea (urea versus glutamine).