Interactions between the 2.4 and 4.2 regions of σS, the stress-specific σ factor of Escherichia coli, and the -10 and -35 promoter elements

The sigma(s) subunit of Escherichia coli RNA polymerase holoenzyme (Esigma(S)) is a key factor of gene expression upon entry into stationary phase and in stressful conditions. The selectivity of promoter recognition by Esigma(S) and the housekeeping Esigma(70) is as yet not clearly understood. We used a genetic approach to investigate the interaction of sigma(S) with its target promoters. Starting with down-promoter variants of a sigma(S) promoter target, osmEp, altered in the -10 or -35 elements, we isolated mutant forms of sigma(S) suppressing the promoter defects. The activity of these suppressors on variants of osmEp and ficp, another target of sigma(S), indicated that sigma(S) is able to interact with the same key features within a promoter sequence as sigma(70). Indeed, (i) sigma(S) can recognize the -35 element of some but not all its target promoters, through interactions with its 4.2 region; and (ii) amino acids within the 2.4 region participate in the recognition of the -10 element. More specifically, residues Q152 and E155 contribute to the strong preference of sigma(S) for a C in position -13 and residue R299 can interact with the -31 nucleotide in the -35 element of the target promoters.