A role for the conserved GAFTGA motif of AAA plus transcription activators in sensing promoter DNA conformation

Transcription from sigma(54)-dependent bacterial promoters can be regarded as a second paradigm for bacterial gene transcription. The initial sigma(54)-RNA polymerase (RNAP)center dot promoter complex, the closed complex, is transcriptionally silent. The transcriptionally proficient sigma(54)-RNAP center dot promoter complex, the open complex, is formed upon remodeling of the closed complex by actions of a specialized activator protein that belongs to the AAA ((A) under bar TPases (a) under bar ssociated with various cellular (a) under bar ctivities) protein family in an ATP hydrolysis-dependent reaction. The integrity of a highly conserved signature motif in the AAA activator (known as the GAFTGA motif) is important for the remodeling activity of the AAA activator and for open complex formation. We now provide evidence that the invariant threonine residue of the GAFTGA motif plays a role in sensing the DNA downstream of the sigma(54)-RNAP-binding site and in coupling this information to sigma(54)-RNAP via the conserved regulatory Region I domain of sigma(54) during open complex formation.