A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo.

sigma 54 is an atypical sigma factor involved in enhancer-dependent transcription in Escherichia coli. In vivo assays were developed for following the kinetics and thermodynamics of sigma 54-dependent melting of the glnAP2 promoter start site. These assays were applied to a series of three sigma 54 polymerases containing zero, one, and two copies of the highly acidic trimer repeat region. The results showed that at least one copy of this acid region is required for a complete melting transition at physiological temperature, but is not required for a low temperature melting transition. The rate of melting the promoter in vivo increased with number of copies of this region. Taken together with other observations, the experiments point to a role for the acid region in triggering conformational changes that lead to specific promoter melting. The acid region is required for these changes to occur fully at physiological temperature and influences the rate at which they occur.