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

Abstract

Classical elements of σ 70 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 σ 70 in double-stranded DNA (dsDNA) form, the downstream bases in the -10 motif ( -11ATAAT -7) are responsible for σ 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 ( -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 σ 70-dsDNA interactions, I found a significantly stronger tendency of this element to complement weak -10 elements that are involved in σ 70-ssDNA interactions. This finding is in contrast to the established view, according to which the -15 element provides a sufficient number of σ 70-dsDNA interactions, and suggests that the main parameter determining a functional promoter is the overall promoter strength. © 2011, American Society for Microbiology.