Transcription from two overlapping gal promoters is repressed by Gal repressor binding to bipartite gal operators, O E and O I, which flank the promoters. Concurrent repression of the gal promoters also requires the bacterial histone‐like protein HU which acts as a co‐factor. Footprinting experiments using iron–EDTA‐coupled HU show that HU binding to gal DNA is orientation specific and is specifically dependent upon binding of GalR to both O E and O I. We propose that HU, in concert with GalR, forms a specific nucleoprotein higher order complex containing a DNA loop. This way, HU deforms the promoter to make the latter inactive for transcription initiation while remaining sensitive to inducer. The example of gal repression provides a model for studying how a ‘condensed’ DNA becomes available for transcription.

Regulation of gene transcription in both prokaryotes and eukaryotes involves formation of various DNA—multiprotein complexes of higher order structure through communication between distant regions of DNA. The communication between distant DNA sites occurs by interaction between proteins bound to the sites by looping out the intervening DNA segments. The repression of transcription of two overlapping promoters of the gal operon in Escherichia coli requires Gal repressor (GalR) and the histone-like protein HU. Both in vivo and in vitro data support a proposed HU containing complex responsive to induction in which GalR molecules bound to two distant operator sites interact by looping out DNA. We successfully applied atomic force microscope (AFM) imaging to visualize gal DNA complexes with proteins. We report GalR mediated DNA looping in which HU plays an obligatory role by helping GalR tetramerization. Supercoiling of DNA, which is also critical for GalR action, may stabilize the DNA loops by providing an energetically favorable geometry of the DNA.