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Nucleic Acids Research, Vol 26, Issue 20 4714-4720, Copyright © 1998 by Oxford University Press

ARTICLES

The two homeodomains of the ZmHox2a gene from maize originated as an internal gene duplication and have evolved different target site specificities

T Kirch, S Bitter, B Kisters-Woike and W Werr
Institut fur Entwicklungsbiologie and Institut fur Genetik, Universitat zu Koln, Gyrhofstrasse 17, 50923 Koln, Germany.

The maize ZmHox2a gene encodes two homeodomains which originated by a 699 bp duplication within an ancestral precursor. The sequences of the two ZmHox2a homeodomains are highly diverged in the N-terminal arm, while residues in the helical part have mostly been conserved. We show here that both ZmHox2a homeodomains are functional DNA-binding motifs but exhibit different target site specificities. CASTing experiments reveal a TCCT motif recognized by HD1 but a GATC tetranucleotide as the recognition sequence of HD2. Mutation of the central nucleotides in both tetranucleotide core motifs abolishes DNA binding. A domain swap experiment indicates that target site specificity is achieved in a combinatorial manner by the contributions of the diverged N-terminal arms together with the slightly different recognition helices. Computer modelling suggests that K47 and H54 in the recognition helices preferentially contact the bases at the 3'-terminus of the tetranucleotide target sequences.
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