Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription

Repressor ω regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ω belongs to homodimeric ribbon-helix-helix (RHH(2)) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω(2) binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-(A)/(T)ATCAC(A)/(T)-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω(2) and contrasting other RHH(2) repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω(2) binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω(2) passes the central C–G base pair of each heptad with ∼0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (→→), ∼0.6 Å shorter in (→←) but would be ∼0.6 Å longer in (←→). These variations grade interactions between adjacent ω(2) and explain modulations in cooperative binding affinity of ω(2) to operators with different heptad orientations.