We have determined the nucleotide sequence of a protozoan aminoacyl-tRNA synthetase. The isoleucyl-tRNA synthetase (ileRS) gene [ilsA; formerly cupC, Martindale, D. W., Martindale, H. M., and Bruns, P. J. (1986) Nucleic Acids Res. 14, 1341-1354] from the ciliate Tetrahymena thermophila was sequenced and found to have eight introns, four transcription start sites, and a putative polypeptide of 1081 amino acids. A polypeptide 20 amino acids longer could be made if a transcribed in-frame ATG close to the start sites and with suboptimal sequence context is used. This gene was identified through hybridization and amino acid sequence similarity to the previously cloned and sequenced ileRS (cytoplasmic) gene from Saccharomyces cerevisiae [Englisch, U., Englisch, S., Markmeyer, P., Schischkoff, J., Sternbach, H., Kratzin, H., and Cramer, F. (1987) Biol. Chem. Hoppe-Seyler 368, 971-979; Martindale, D. W., Gu, Z. M., and Csank, C. (1989) Curr. Genet. 15, 99-106] with which it shares 47% of its amino acids. We also compared it to ileRS genes from E. coli and an archaebacterium. Two leucine zippers motifs were identified in the carboxyl-terminal domain of the polypeptide; one of these motifs is in the same area as the zinc finger motif found in the E. coli enzyme. The transcription pattern of the ilsA gene was monitored under various culture conditions and parallels changes in protein synthesis.