BINDING OF THE FUR (FERRIC UPTAKE REGULATOR) REPRESSOR OF ESCHERICHIA-COLI TO ARRAYS OF THE GATAAT SEQUENCE

The mode of DNA binding of the Fur (ferric uptake regulator) repressor which controls transcription of iron-responsive genes in Escherichia coli, has been re-examined. Using as a reference the known sites at th e promoter of the aerobactin operon of Escherichia coli, we have compa red in detail the patterns of interaction between the purified Fur pro tein and natural or synthetic DNA targets. DNase I and hydroxyl radica l footprinting, as well as missing-T assays, consistently revealed tha t functional Fur sites are composed of a minimum of three repeats of t he hexameric motif GATAAT rather than by a palindromic 19 bp target se quence. Extended binding sites, constructed by stepwise addition of on e or hive direct repeats of the same sequence, were occupied co-operat ively by Fur with the same pattern of interactions as those observed w ith the core of three repeats. This indicated that functional sites wi th a range of affinities can be formed by the addition of discrete GAT AAT extensions to a minimal recognition sequence. The fashion in which Fur binds its target, virtually unknown in prokaryotic transcriptiona l regulators, accounts for the observed helical wrapping of the protei n around the DNA helix. (C) 1998 Academic Press.