Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix-turn-helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes.Pax genes play key roles in regulating developmental processes and are characterized by a conserved motif, the paired box, which encodes the paired domain (PD; ref. 1). The PD is a DNA-binding domain (2) that is composed of two separable and independent subdomains, the N-terminal PAI and the C-terminal RED domains (3, 4), each containing a helix-turnhelix (HTH) motif (5). The PAI domain seems to be the most critical part of the PD (2, 5), because it is necessary and sufficient for DNA binding in vitro (2-4, 6). In fact, the Drosophila Prd protein does not need the RED domain to confer full function to the protein in vivo (7,8). There are, however, situations in which the RED domain may play a role (3). The bipartite organization of the PD allows for the recognition of composite sites by both PAI and RED domain. Furthermore, there is an isoform of the Pax-6 protein (Pax-6 5a) that contains, in the middle of the recognition helix of the PAI domain, an 11-residue insertion that inactivates DNA binding to sequences normally bound by the Pax-6 PD (6). Pax-6 5a, however, is able to bind to a recently described sequence called 5aCON (6). Other Pax proteins also contain insertions in the PAI domain that inactivate DNA binding and uncover RED-domain DNA-binding activity (9). However, to date, there has been no report of a Pax protein containing only a PAI or a RED domain.About half of the known Pax genes (1, 10-16) also encode a second DNA-binding domain, a Prd-class homeodomain (HD). The Prd-class HDs recognize DNA through cooperative dimerization mediated by the HD (17, 18). There are several Prd HD subclasses that are...
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