Gene transcription is regulated through the interactions of RNA polymerase (RNAP) with transcription factors, such as the bacterial σ proteins. We have devised a new strategy that relies on targeted protein footprinting to make an extensive survey of proximity to the protein surface. This involves attaching cutting reagents randomly to lysine residues on the surface of a protein such as σ. The lysine-labeled σ protein is then used to cleave the polypeptide backbones of the RNAP proteins at exposed residues adjacent to the σ binding site. We used targeted protein footprinting to compare the areas near which σ70, σ54, σ38, σ(E), NusA, GreA, and omega bind to the protein subunits of Escherichia coli RNAP. The σ proteins and NusA cut sites in similar regions of the two large RNAP subunits, β and β', outlining a common surface. GreA cuts a larger set of sites, whereas omega shows no overlap with the others, cutting only the β' subunit at a unique location.
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