FORMATION OF A MONOMERIC DNA-BINDING DOMAIN BY SKN-1 BZIP AND HOMEODOMAIN ELEMENTS

Maternally expressed Skn-1 protein is required for the correct specifi cation of certain blastomere fates in early Caenorhabditis elegans emb ryos. Skn-1 contains a basic region similar to those of basic leucine zipper (bZIP) proteins but, paradoxically, it lacks a leucine zipper d imerization segment. Random sequence selection methods were used to sh ow that Skn-1 binds to specific DNA sequences as a monomer. The Skn-1 basic region lies at the carboxyl terminus of an 85-amino acid domain that binds preferentially to a bZIP half-site and also recognizes adja cent 5' AT-rich sequences in the minor groove, apparently with an amin o (NH2)-terminal ''arm'' related to those of homeodomain proteins. The intervening residues appear to stabilize interactions of these two su bdomains with DNA. The Skn-1 DNA binding domain thus represents an alt ernative strategy for promoting binding of a basic region segment reco gnition helix to its cognate half-site. The results point to an underl ying modularity in subdomains within established DNA binding domains.