Interactions among GalR-binding sites on bacterial DNA

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Our understanding of DNA packaging in bacteria remains obscure, as no unifying mechanism, such as that in eukaryotes, has been described. In addition, many transcription events require that remote sites on the DNA come together in a well defined configuration. The mechanism behind such events and the possible ancillary proteins are not known. The GalR protein is known to bind DNA operator sites to accomplish galactose gene regulation in E-coli, and even more strongly in the presence of another protein, HU, which is known to effect DNA bending. The abundance of both proteins in E-coli and the existence of multiple GalR binding sites on its chromosome, motivate the hypothesis that GalR is a central actor in bridging remote DNA sites, thus acting in a dual role of a DNA packaging agent and of a protein ancillary to transcription events. A combination of biochemical and imaging methods are employed. Fluorescently tagged GalR are visualized in vivo and complexes of GalR with supercoiled plasmids of various sizes and carrying a number of GalR binding sites are visualized at a single molecule level. We use atomic force microscopy for the latter and we can clearly see the effects of protein binding. Measurements of loop sizes before and after protein binding clearly support the hypothesis that GalR oligomers of various sizes bridge remote DNA sites.