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

摘要

Repressor omega regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. omega belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel beta-sheet for DNA major groove binding. Homodimeric omega(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 omega(2) and contrasting other RHH2 repressors, to non-palindromic direct (->->) repeats. Here we investigate with crystal structures how omega(2) binds specifically to heptads in minimal operators with (->->) and (-><-) repeats. Since the pseudo-2-fold axis relating the monomers in omega(2) passes the central C-G base pair of each heptad with similar to 0.3 angstrom downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (->->), similar to 0.6 angstrom shorter in (-><-) but would be similar to 0.6 angstrom longer in (<-->). These variations grade interactions between adjacent omega(2) and explain modulations in cooperative binding affinity of omega(2) to operators with different heptad orientations.