Transcription initiation involves the coordinated activities of large multimeric complexes, but little is known about their biogenesis. Here we report several principles underlying the assembly and topological organization of the highly conserved SAGA and NuA4 co-activator complexes, which share the Tra1 subunit. We show that Tra1 contributes to the overall integrity of NuA4, whereas, within SAGA, it specifically controls the incorporation of the de-ubiquitination module (DUB), as part of an ordered assembly pathway. Biochemical and functional analyses reveal the mechanism by which Tra1 specifically interacts with either SAGA or NuA4. Finally, we demonstrate that Hsp90 and its cochaperone TTT promote Tra1 de novo incorporation into both complexes, indicating that Tra1, the sole pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the assembly of transcriptional complexes and reveals the contribution of dedicated chaperones to this process.

Highlights d The Hsp90 cochaperone TTT recognizes PIKKs cotranslationally d TTT binds to the structurally related FATKIN unit d Nascent PIKKs remain in a non-native state until translation is completed d The cotranslational maturation of PIKKs precedes their assembly into larger complexes

Transcription initiation involves the coordinated activities of large multimeric complexes.Little is known about the mechanisms and pathways that drive their assembly from individual components. We report here several principles underlying the assembly of the highly conserved SAGA co-activator complex, which is composed of 19 subunits organized into functional modules. First, we demonstrate that SAGA assembles through an ordered pathway, in which the core subunit Spt20 recruits Tra1, which then promotes the incorporation of the de-ubiquitination module (DUB). Second, affinity purifications and phenotypic analyses identified a small region of Spt20 that is both necessary and sufficient to anchor Tra1 to SAGA. Third, Tra1 is shared with the NuA4 co-activator complex and is the only pseudokinase of the PIKK family. We accumulated functional and biochemical evidence that Tra1 shares a specific Hsp90 cochaperone with PIKKs, the Triple-T complex, for its cotranslational folding and de novo incorporation into both SAGA and NuA4. Finally, in contrast to its specific role in SAGA assembly, Tra1 contributes to scaffold the entire NuA4 complex. Overall, our study brings mechanistic insights into the de novo assembly of transcriptional complexes via ordered pathways and reveals the contribution of dedicated chaperones to this process.

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