The amino terminus of Salmonella enterica serovar typhimurium σ54 is required for interactions with an enhancer-binding protein and binding to fork junction DNA

Transcription initiation by the alpha(54)-RNA polymerase holoenzyme requires an enhancer-binding protein that is thought to contact alpha(54) to activate transcription. To identify potential enhancer-binding protein contact sites in alpha(54), we compared the abilities of wild-type and truncated forms of Salmonella enterica serovar Typhimurium alpha(54) to interact with the enhancer-binding protein DctD in a chemical cross-linking assay. Removal of two regions in the amino-terminal portion of alpha(54), residues 57 to 105 and residues 144 to 179, prevented crosslinking? but removal of either region alone did not. In addition, deletion of 56 amino-terminal residues of alpha(54) (region I) reduced the affinity of the protein for a fork junction DNA probe.