Abstract: The Tra1 protein is a direct transcription activator target that is essential for coactivator function of both the SAGA and NuA4 histone acetyl transferase (HAT) complexes. The approximately 400 kDa S. cerevisiae Tra1 polypeptide and its human counterpart TRRAP contain 67-68 tandem alpha-helical HEAT and TPR protein repeats that extend from the N-terminus to the conserved yet catalytically inactive PI3K kinase domain. We generated a series of mutations spanning the length of the protein and assayed for defects in transcription, coactivator recruitment, and histone acetylation at SAGA and NuA4-dependent genes. Inviable TRA1 mutants all showed defects in SAGA and NuA4 complex stability, suggesting that similar surfaces of Tra1 mediate assembly of these two very different coactivator complexes. Nearly all of the viable Tra1 mutants showed transcription defects that fell into one of three classes: (1) defective recruitment to promoters, (2) reduced stability of the SAGA and NuA4 HAT modules, or (3) normal recruitment of Tra1-associated subunits but reduced HAT activity in vivo. Our results show that Tra1 recruitment at Gcn4-dependent and Rap1-dependent promoters requires the same regions of Tra1, and that separate regions of Tra1 contribute to the HAT activity and stability of the SAGA and NuA4 HAT modules.