Footprint of the sigma protein.

Escherichia coli RNA Polymerase is a multi-subunit enzyme that catalyzes RNA synthesis, using DNA as a template. The sigma subunit of this enzyme plays an important role in the recognition of promoter sites on DNA. Using DNase I footprinting, we have found that in the absence of the other subunits, sigma binds specifically to the bacteriophage lambda PR promoter DNA sequence. In the presence of the sigma subunit alone, a protective footprint encompassing the region between residue positions -41 and +17 was observed (where +1 is the transcription start site). The holoenzyme gave a footprint covering the same region. Thus not only does the sigma subunit interact with the DNA promoter site in the absence of the other components of RNA polymerase, but also the footprint of sigma is indistinguishable from that of the holoenzyme.