Growth Environments

The 203 transcriptional regulators were identified by searching the YPD and MIPS databases (Mewes et al. 1997; Hodges et al. 1999; Costanzo et al. 2001) for known and predicted transcription factors and nucleic acid binding proteins. Regulators were selected for profiling in a specific environment if they were essential for growth in that environment or if there was other evidence implicating them in regulation of gene expression in that environment.

A brief description of the environmental conditions used follows:

Rich media. Cells were grown in YPD (1% yeast extract/2% peptone/2% glucose) to an OD600 of ~0.8.

Highly hyperoxic. Cells were grown in YPD to an OD600 of ~0.5 followed by treatment with hydrogen peroxide (4 mM final) for 30 minutes.

Moderately hyperoxic. Cells were grown in YPD to an OD600 of ~0.5 followed by treatment with hydrogen peroxide (0.4 mM final) for 20 minutes.

Amino acid starvation. Cells were grown to an OD600 of ~0.6 in synthetic complete medium followed by treatment with the inhibitor of amino acid biosynthesis sulfometuron methyl (0.2 mg/ml final) for two hours.

Nutrient deprived. Cells were grown in YPD to an OD600 of ~0.8 followed by treatment with rapamycin (100 nM final) for 20 minutes.

Filamentation inducing. Cells were grown in YPD containing 1% butanol for either 90 minutes or 14 hours (corresponding to an OD600 of ~0.8).

Mating inducing. Cells were grown in YPD to an OD600 of ~0.8 followed by treatment with the alpha factor pheromone (5 mg/ml) for 30 minutes.

Elevated temperature. Cells were grown in YPD at 30∞C to an OD600 of ~0.5 followed by a temperature shift to 37∞C for 45 minutes.

Galatose medium. Cells were grown in YEP medium supplemented with galactose (2%) to an OD600 of ~0.8.

Raffinose medium. Cells were grown in YEP medium supplemented with raffinose (2%) to an OD600 of ~0.8.

Acidic medium. Cells were grown in YPD to an OD600 of ~0.5 followed by treatment for 30 minutes with succinic acid (0.05 M final) to reach a pH of 4.0.

Phosphate deprived medium. Cells were grown in synthetic complete medium lacking phosphate to a final OD of ~0.8.

Vitamin deprived medium. Cells were grown in synthetic complete medium lacking thiamin to a final OD of ~0.8.