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

Classical elements of sigma(70) 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 (T-12) interact with sigma(70) in double-stranded DNA (dsDNA) form, the downstream bases in the -10 motif ((-11)ATAAT(-7)) are responsible for sigma(70)-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 T-15. 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 sigma(70)-dsDNA interactions, I found a significantly stronger tendency of this element to complement weak -10 elements that are involved in sigma(70)-ssDNA interactions. This finding is in contrast to the established view, according to which the -15 element provides a sufficient number of sigma(70)-dsDNA interactions, and suggests that the main parameter determining a functional promoter is the overall promoter strength.