RNA polymerase holoenzymes can share a single transcription start site for the Pm promoter -: Critical nucleotides in the -7 to -18 region are needed to select between RNA polymerase with σ38 or σ32

The Pm promoter of the benzoate meta-cleavage pathway is transcribed with E sigma(32) or E sigma(38) according to the growth phase, with an identical transcriptional start site. To investigate sequence determinants in the interaction between either of the two RNA polymerases and Pm, all possible single mutants between positions -7 and -18 were generated, and the activity in the exponential and stationary phases of the resulting mutant promoters was compared. The results precisely delimited a-10 element between positions -7 and -12 (TAGGCT), which defined a promoter sharing nucleotides with both sigma(38) and sigma(32) consensus. The first two and the last positions of this hexamer were crucial for recognition by both polymerases. Position -10 was the only one specifically recognized by E sigma(38), whereas positions -8, -9, and the C-track between positions -14 and -17 were important for specific E sigma(32) recognition. Western blots showed that sigma(32) was only detectable in the exponential phase, and sigma(38) appeared in the early stationary phase. In the rpoH mutant KY1429, sigma(38) was already present in the exponential growth phase both free and bound to the RNA polymerase core, in good correlation with the transcription levels found. Pm seems to be optimized for recognition by sigma(32) as an initial response to the addition of effector to the medium and allows binding of the adaptable sigma(38)-dependent RNA polymerase in the stationary phase. XylS is always required for Pm transcription. Therefore, the mechanism that controls Pm expression involves specific nucleotide sequences, the abundance of free and core-bound sigma(32) and sigma(38) factors during growth, and the presence of the regulator activated by an effector.