Potassium permanganate susceptibility of sigma E-RNA polymerase-promoter complexes

We used potassium permanganate (KMnO4) to identify unpaired thymidine (T) residues in promoter complexes formed by RNA polymerase (RNAP) associated with sigma E (sigma E-RNAP) from Bacillus subtilis. We found that a region of the spoIIID promoter from at least -10 to +1 becomes melted in the presence of this polymerase. In promoter complexes formed by RNAP associated with a mutant sigma E that melts promoter DNA inefficiently, we noted additional KMnO4 sensitivity at the -11 position of the spoIIID promoter. We suggest that the base pair at -11 is unpaired in both mutant and wild type (wt) complexes; however, close proximity of wt sigma E-RNAP with the T at -11 may protect it from KMnO4 attack. The absence of a close contact between the mutant sigma E-RNAP and the base at -11 may explain why this polymerase uses promoters less efficiently than wt sigma E-RNAP.