The flow of amino acids to both protein and DNA synthesis is particularly important during periods of rapid cell proliferation such as the fetal stages of life. The changes in mRNA levels caused by the different types of growth arrest were studied in F9 embryonal carcinoma cells. The cells were grown in medium deficient in the amino acid lysine or in one containing phosphonoacetyl L-aspartic acid (PALA), which inhibits the incorporation of aspartic acid into pyrimidine nucleotides. A number of mRNAs known to be elevated in growth arrested cells (gas and gadd) were studied by Northern blotting. Samples of RNA from the cells were also compared by differential display reverse transcription-polymerase chain reaction (DDRT-PCR). The results showed that lysine deficiency increased the steady-state levels of a number of mRNAs by 5- to 40-fold. In contrast, the changes in cells treated with PALA were much smaller and less pronounced. Amino acid deficiency induced the mRNAs coding for gadd153 (CHOP-10), gas5, the mouse doublesex-related gene (Dmrt1) and the polyamine modulated factor (PA-1) as well as a number of unidentified expressed sequence tags (EST). These mRNAs were all induced within 24 h of exposure to amino acid deficiency. These very different transcriptional responses may be important in understanding the interactions between protein quantity and quality in different physiologic situations.