DID HOMEODOMAIN PROTEINS DUPLICATE BEFORE THE ORIGIN OF ANGIOSPERMS, FUNGI, AND METAZOA

Homeodomain proteins are transcription factors that play a critical ro le in early development in eukaryotes. These proteins previously have been classified into numerous subgroups whose phylogenetic relationshi ps are unclear. Our phylogenetic analysis of representative eukaryotic sequences suggests that there are two major groups of homeodomain pro teins, each containing sequences from angiosperms, metazoa, and fungi. This result, based on parsimony and neighbor-joining analyses of prim ary amino acid sequences, was supported by two additional features of the proteins. The two protein groups are distinguished by an insertion /deletion in the homeodomain, between helices I and II. In addition, a n amphipathic alpha-helical secondary structure in the region N termin al of the homeodomain is shared by angiosperm and metazoan sequences i n one group. These results support the hypothesis that there was at le ast one duplication of homeobox genes before the origin of angiosperms , fungi, and metazoa. This duplication, in turn, suggests that these p roteins had diverse functions early in the evolution of eukaryotes. Th e shared secondary structure in angiosperm and metazoan sequences poin ts to an ancient conserved functional domain.