Subunit dynamics and nucleotide-dependent asymmetry of an AAA⁺ transcription complex

Bacterial enhancer binding proteins (bEBPs) are transcription activators that belong to the AAA⁺ protein family. They form higher-order self-assemblies to regulate transcription initiation at stress response and pathogenic promoters. The precise mechanism by which these ATPases utilize ATP binding and hydrolysis energy to remodel their substrates remains unclear. Here we employed mass spectrometry of intact complexes to investigate subunit dynamics and nucleotide occupancy of the AAA⁺ domain of one well-studied bEBP in complex with its substrate, the σ⁵⁴ subunit of RNA polymerase. Our results demonstrate that the free AAA⁺ domain undergoes significant changes in oligomeric states and nucleotide occupancy upon σ⁵⁴ binding. Such changes likely correlate with one transition state of ATP and are associated with an open spiral ring formation that is vital for asymmetric subunit function and interface communication. We confirmed that the asymmetric subunit functionality persists for open promoter complex formation using single-chain forms of bEBP lacking the full complement of intact ATP hydrolysis sites. Outcomes reconcile low- and high-resolution structures and yield a partial sequential ATP hydrolysis model for bEBPs.