Redefining Escherichia coli σ70 Promoter Elements: ?15 Motif as a Complement of the ?10 Motif

摘要

Classical elements of σ70 bacterial promoters include the ?35 element (?35TTGACA?30), the ?10 element (?12TATAAT?7), and the extended ?10 element (?15TG?14). Although the ?35 element, the extended ?10 element, and the upstream-most base in the ?10 element (?12T) interact with σ70 in double-stranded DNA (dsDNA) form, the downstream bases in the ?10 motif (?11ATAAT?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 (?15TGnT?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 ?13G and a high degeneracy at ?15T. 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.