To better understand the regulation of gene expression by amino acids, we studied the effects of these macronutrients on fatty acid synthase (FAS), an enzyme crucial for energy storage. When HepG2 cells were fed serum-free media selectively deficient in each amino acid, the omission of any single classic essential amino acid as well as Arg or His (essential in some rapidly growing cells) resulted in FAS mRNA levels that were about half of those in complete medium. Control message levels were unaffected and omission of nonessential amino acids did not alter FAS expression. FAS mRNA levels peaked 12-16 h after feeding complete and Ser (nonessential)-deficient media but did not increase in cells fed Lys (essential)-deficient medium. With Lys, FAS mRNA increased over the physiologic concentration range of 15-150 μM, and low concentrations of lysine decreased FAS but not apoB protein mass. Transcription inhibitors mimicked treatment with Lys-deficient media, and nuclear run-off assays showed that Lys-deficient media abolished FAS but not apoB transcription. After treatment with Lys-deficient media, the intracellular Lys pool was rapidly depleted in association with an increase of uncharged (deacylated) tRNA(Lys) from < 1 to 64% of available tRNA(Lys). Even in the presence of the essential amino acid His, increasing the levels of uncharged tRNA(His) with histidinol, a competitive inhibitor of the histidinyl-tRNA synthetase, blocked FAS expression. Tyrosinol treatment did not alter FAS mRNA levels. These results suggest that essential amino acids regulate FAS expression by altering uncharged tRNA levels, a novel mechanism for nutrient control of gene expression in mammalian cells.