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Molecular and Cellular Biology, October 2000, p. 7673-7684, Vol. 20, No. 20
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Reprogrammable Recognition Codes in Bicoid Homeodomain-DNA Interaction

Vrushank Dave,1 Chen Zhao,1 Fan Yang,1 Chang-Shung Tung,2 and Jun Ma1,*

Division of Developmental Biology, Children's Hospital Research Foundation, Cincinnati, Ohio 45229,1 and Theoretical Biology and Biophysics (T-10), Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 875452

Received 17 March 2000/Returned for modification 1 May 2000/Accepted 18 July 2000

We describe experiments to determine how the homeodomain of the Drosophila morphogenetic protein Bicoid recognizes different types of DNA sequences found in natural enhancers. Our chemical footprint analyses reveal that the Bicoid homeodomain makes both shared and distinct contacts with a consensus site A1 (TAATCC) and a nonconsensus site X1 (TAAGCT). In particular, the guanine of X1 at position 4 (TAAGCT) is protected by Bicoid homeodomain. We provide further evidence suggesting that the unique arginine at position 54 (Arg 54) of the Bicoid homeodomain enables the protein to recognize X1 by specifically interacting with this position 4 guanine. We also describe experiments to analyze the contribution of artificially introduced Arg 54 to DNA recognition by other Bicoid-related homeodomains, including that from the human disease protein Pitx2. Our experiments demonstrate that the role of Arg 54 varies depending on the exact homeodomain framework and DNA sequences. Together, our results suggest that Bicoid and its related homeodomains utilize distinct recognition codes to interact with different DNA sequences, underscoring the need to study DNA recognition by Bicoid-class homeodomains in an individualized manner.

* Corresponding author. Mailing address: Division of Developmental Biology, Children's Hospital Research Foundation, 3333 Burnet Ave., Cincinnati, OH 45229. Phone: (513) 636-7977. Fax: (513) 636-4317. E-mail: jun.ma{at}chmcc.org.

Molecular and Cellular Biology, October 2000, p. 7673-7684, Vol. 20, No. 20
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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