Using PCR we have isolated two novel, closely related cDNA clones coding for a GTP-binding low-M(r) protein from Tetrahymena cells. The two clones from T. thermophila and T. pyriformis have open reading frames encoding proteins of 225 amino acids (aa) with a calculated M(r) of 25,648, and of 223 aa with a calculated M(r) of 25,421, respectively. The two gene products were very homologous to Ran/TC4 which are involved in chromatin condensation and control of the cell cycle: they possess much higher similarities to human, chicken, Schizosaccharomyces pombe and Dictyostelium discoideum Ran/TC4 homologues than those to other GTP-binding low-M(r) proteins, such as Ras and Rho. Thus, the two clones isolated from Tetrahymena were designated as Tt-ran and Tp-ran, respectively. Tt-ran and Tp-ran share 83% identity at nucleotide level, and about 92% identity and 94% homology at aa level. Tt- and Tp-Ran, as well as other Ran/TC4, contain the four consensus regions involved in GTP/GDP-binding and GTPase activities. However, at the C-terminal end, although all the known Ran/TC4 terminate in a consensus D-L motif, Tt-Ran and Tp-Ran do not have the unique aa sequence of other Ran/TC4, but have a F-N motif. Tt-ran and Tp-ran were actively transcribed in vivo as a 1.0-kb mRNA.