COOPERATIVE INTERACTIONS BETWEEN PAIRED DOMAIN AND HOMEODOMAIN

The Pax proteins are a family of transcriptional regulators involved i n many developmental processes in all higher eukaryotes. They are char acterized by the presence of a paired domain (PD), a bipartite DNA bin ding domain composed of two helix-turn-helix (HTH) motifs, the PAI and RED domains, The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA, Many of t hese proteins therefore contain three HTH motifs each able to recogniz e DNA, However, all PDs recognize highly related DNA sequences, and mo st HDs also recognize almost identical sites, We show here that differ ent Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired pro tein can bind, in vitro, exclusively through its PAI domain, or throug h a dimer of its HD, or through cooperative interaction between PAI do main and HD, However, prd function in vivo requires the synergistic ac tion of both the PAI domain and the HD. Pax proteins with only a PD ap pear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expand ing their recognition repertoire.