Target selectivity of bicoid is dependent on nonconsensus site recognitionand protein-protein interaction

We describe experiments to compare the activities of two Drosophila homeodo main proteins, Bicoid (Bcd) and an altered-specificity mutant of Fushi tara zu, Ftz(Q50K). Although the homeodomains of these proteins share a virtuall y indistinguishable ability to recognize a consensus Bcd site, only Bcd can activate transcription from natural enhancer elements when assayed in both yeast and Drosophila Schneider S2 cells. Our analysis of chimeric proteins suggests that both the homeodomain of Bcd and sequences outside the homeod omain contribute to its ability to recognize natural enhancer elements. We further show that, unlike the Bcd homeodomain, the Ftz(Q50K) homeodomain fa ils to recognize nonconsensus sites found in natural enhancer elements. The defect of a chimeric protein containing the homeodomain of Ftz(Q50K) in pl ace of that of Bcd can be preferentially restored by converting the noncons ensus sites in natural enhancer elements to consensus sites. Our experiment s suggest that the biological specificity of Bcd is determined by combinato rial contributions of two important mechanisms: the nonconsensus site recog nition function conferred by the homeodomain and the cooperativity function conferred primarily by sequences outside the homeodomain. A systematic com parison of different assay methods and enhancer elements further suggests a fluid nature of the requirements for these two Bcd functions in target sel ection.