Volatile ammonia functions as a long range alarm signal important for the transition of yeast colonies to their adaptive alkali developmental phase and for their consequent long term survival. Cells of aged Saccharomyces cerevisiae sok2 colonies deleted in the gene for Sok2p transcription factor are not able to release a sufficient amount of ammonia out of the cells, they are more fragile than cells of wild type colonies, and they exhibit a survival defect. Genome-wide analysis on gene expression differences between sok2 and WT colonies revealed that sok2 colonies are not able to switch on the genes of adaptive metabolisms effectively and display unbalanced expression and activity of various enzymes involved in cell protection against oxidative damage. Impaired amino acid metabolism and insufficient activation of genes for putative ammonium exporters Ato and of those for some other membrane transporters may be responsible for observed defects in ammonia production. Thus, Sok2p appears to be an important regulator of S. cerevisiae colony development. Gene expression differences caused by its absence in colonies differ from those described previously in liquid cultures, which suggests a pleiotropic effect of Sok2p under different conditions.