SYNERGISM IN DNA-BINDING OF PAIRED AND HO MEO DOMAINS IN PAX PROTEIN

The Pax genes encode a set of transcriptional regulators involved in s everal developmental processes. They are characterized by the presence of the paired domain (PD), a DNA binding domain composed of two Helix -Turn-Helix (HTH) motifs, the PAI and RED domains. Some Pax proteins c ontain a third HTH DNA binding motif, the homeodomain (HD). Since all PDs recognize highly related DNA sites, and since all HDs recognize a common TAAT sequence, it has been difficult to understand how these pr oteins achieve their functional specificity. Here, we describe how dif ferent Pax proteins use multiple combinations of their DNA binding mot ifs to target different promoters. In vitro, the Drosophila paired pro tein can bind either through its PAI domain, through its HD via cooper ative dimerization, or through both domains. In vivo, using a transgen ic rescue assay, we show that prd function requires the synergistic ac tion of both the PAI domain and the HD on abutted PD and HD sites. Sur prisingly, the RED domain, although conserved, can be deleted without loss of viability. This is in contrast to other Pax proteins that requ ire both PAI and RED domains. Furthermore, specific isoforms of Pax6 a s well as a ne iv Pax protein, Lune, may rely on the RED domain alone. Finally, we propose that Pax6 may also act through its HD alone on a series of highly conserved palindromic TAAT sites found in all rhodops in promoters. This may represent the ancient function of this master r egulator of eye development before it acquired a PD.