Redefining Escherichia coli σ 70 Promoter Elements: −15 Motif as a Complement of the −10 Motif

Classical elements of σ70 bacterial promoters include the −35 element (−35 TTGACA−30 ), the −10 element (−12 TATAAT−7 ), and the extended −10 element (−15 TG−14 ). Although the −35 element, the extended −10 element, and the upstream-most base in the −10 element (−12 T) interact with σ70 in double-stranded DNA (dsDNA) form, the downstream bases in the −10 motif (−11 ATAAT−7 ) are responsible for σ70 -single-stranded DNA (ssDNA) interactions. In order to directly reflect this correspondence, an extension of the extended −10 element to a so-called −15 element (−15 TGnT−12 ) has been recently proposed. I investigated here the sequence specificity of the proposed −15 element and its relationship to other promoter elements. I found a previously undetected significant conservation of−13 G and a high degeneracy at−15 T. I therefore defined the −15 element as a degenerate motif, which, together with the conserved stretch of sequence between −15 and −12, allows treating this element analogously to −35 and −10 elements. Furthermore, the strength of the −15 element inversely correlates with the strengths of the −35 element and −10 element, whereas no such complementation between other promoter elements was found. Despite the direct involvement of −15 element in σ70 -dsDNA interactions, I found a significantly stronger tendency of this element to complement weak −10 elements that are involved in σ70 -ssDNA interactions. This finding is in contrast to the established view, according to which the −15 element provides a sufficient number of σ70 -dsDNA interactions, and suggests that the main parameter determining a functional promoter is the overall promoter strength.