Unambiguous TATA boxes have not been identified in upstream sequences of Tetrahymena thermophila genes analyzed to date. To begin a characterization of the promoter requirements for RNA polymerase II, the gene encoding TATA-binding protein (TBP) was cloned from this species. The derived amino acid sequence for the conserved C-terminal domain of Tetrahymena TBP is one of the most divergent described and includes a unique 20-amino-acid C-terminal extension. Polyclonal antibodies generated against a fragment of Tetrahymena TBP recognize a 36-kDa protein in macronuclear preparations and also cross-react with yeast and human TBPs.Immunocytochemistry was used to examine the nuclear localization of TBP during growth, starvation, and conjugation (the sexual phase of the life cycle). The transcriptionaily active macronuclei stained at all stages of the life cycle. The transcriptionally inert micronuclei did not stain during growth or starvation but surprisingly stained with anti-TBP throughout early stages of conjugation. Anti-TBP staining disappeared from developing micronuclei late in conjugation, corresponding to the onset of transcription in developing macronuclei. Since micronuclei do not enlarge or divide at this time, loss of TBP appears to be an active process. Thus, the transcriptional differences between macro-and micronuclei that arise during conjugation are associated with the loss of a major component of the basal transcription apparatus from developing micronuclei rather than its appearance in developing macronuclei.TATA-binding protein (TBP) is required for transcription by all three nuclear RNA polymerases. TBP, along with an assortment of distinct TBP-associated factors, has been found to make up the RNA polymerase I selectivity factor I (9, 36), the polymerase II general transcription factor IID (14,73,83), and the RNA polymerase III general transcription factor IIIB (38,43,62,72,75). Given the need for TBP to function in these different complexes in such fundamental cellular processes, it is not surprising that TBP is highly conserved throughout eukaryotes. Yeast and human TBP are functionally interchangeable in basal transcription reactions reconstituted with yeast or human components (5,17,39) and have nearly identical TATA element binding specificities (78). The C-terminal 180 residues of TBP from a variety of organisms are typically 80% identical in amino acid sequence, whereas the N-terminal regions are divergent both in length and in amino acid sequence (6, 16, 20, 26, 28-30, 33, 37, 49, 55, 61). The C-terminal domain is necessary and sufficient for TATA element binding and basal transcription in vitro (28,41,55) and for the essential functions of yeast TBP in yeast cells (10,21,57,84). This region forms an independent structural domain within the context of the intact protein (41). It contains an interrupted repeat of 67 amino acids, a short basic repeat, and a region weakly homologous with bacterial sigma factors (10, 80). In addition to its role in the basal transcription apparatus, TBP also ...