Transcription factor IID (TFIID) plays a key role in regulating eukaryotic gene expression by directly binding promoters and enhancer-bound transactivator proteins. However, the precise mechanisms and outcomes of transactivator-TFIID interaction remain unclear. Transcription of yeast ribosomal protein genes requires TFIID and the DNA-binding transactivator Rap1. We have previously shown that Rap1 directly binds to the TFIID complex through interaction with its TATA-binding proteinassociated factor (Taf) subunits Taf4, -5, and -12. Here, we identify and characterize the Rap1 binding domains (RBDs) of Taf4 and Taf5. These RBDs are essential for viability but dispensable for Taf-Taf interactions and TFIID stability. Cells expressing altered Rap1 binding domains exhibit conditional growth, synthetic phenotypes when expressed in combination or with altered Rap1, and are selectively defective in ribosomal protein gene transcription. Taf4 and Taf5 proteins with altered RBDs bind Rap1 with reduced affinity. We propose that collectively the Taf4, Taf5, and Taf12 subunits of TFIID represent the physical and functional targets for Rap1 interaction and, furthermore, that these interactions drive ribosomal protein gene transcription.
Activation of eukaryotic RNA polymerase II (pol II)2 -transcribed genes requires the action of an ensemble of proteins collectively referred to as coactivators (1, 2). These large multisubunit protein assemblies stimulate mRNA gene transcription at several distinct steps as follows: either by utilizing intrinsic enzymatic activities to alter the biochemical characteristics of transcription proteins and/or chromatin; facilitating accurate formation of preinitiation complexes (PICs) near the transcription start site; stimulating pol II activity; or by serving as scaffolds for the assembly of additional coactivators on target genes. Many variations of these mechanisms have been described, but it is generally accepted that coactivators are targeted by gene-specific enhancer-bound transactivator proteins. Transactivators are minimally composed of distinct DNA binding domains (DBDs) and activation domains (ADs). Classical studies have shown that ADs enhance transcription rates by directly stimulating the formation and/or function of the PIC, which is an assortment of over 40 distinct polypeptides often termed the general transcription factors