Role of the spacer between the −35 and −10 regions in σs promoter selectivity in Escherichia coli


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In vitro, the σs subunit of RNA polymerase (RNAP), RpoS, recognizes nearly identical −35 and −10 promoter consensus sequences as the vegetative σ70. In vivo, promoter selectivity of RNAP holoenzyme containing either σs (Eσs) or σ70 (Eσ70) seems to be achieved by the differential ability of the two holoenzymes to tolerate deviations from the promoter consensus sequence. In this study, we suggest that many natural σs-dependent promoters possess a −35 element, a feature that has been considered as not conserved among σs-dependent promoters. These −35 hexamers are mostly non-optimally spaced from the −10 region, but nevertheless functional. A ± 2 bp deviation from the optimal spacer length of 17 bp or the complete absence of a −35 consensus sequence decreases overall promoter activity, but at the same time favours Eσs in its competition with Eσ70 for promoter recognition. On the other hand, the reduction of promoter activity due to shifting of the −35 element can be counterbalanced by an activity-stimulating feature such as A/T-richness of the spacer region without compromising Eσs selectivity. Based on mutational analysis of σs, we suggest a role of regions 2.5 and 4 of σs in sensing sub-optimally located −35 elements.