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

• Published in: Nucleic acids research Vol. 34; no. 5; pp. 1450 - 1458
• Main Authors: Weihofen, Wilhelm Andreas, Cicek, Aslan, Pratto, Florencia, Alonso, Juan Carlos, Saenger, Wolfram
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 2006
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; Crystallography, X-Ray; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Gene Expression Regulation, Bacterial; Models, Molecular; Operator Regions, Genetic; Protein Binding; Protein Structure, Secondary; Repetitive Sequences, Nucleic Acid; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism; Sequence Deletion; Threonine - chemistry; Transcription, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkl015

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 (RHH2) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-A/TATCACA/T-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω2 and contrasting other RHH2 repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω2 binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω2 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 ω2 and explain modulations in cooperative binding affinity of ω2 to operators with different heptad orientations.