Homeodomain revisited: a lesson from disease-causing mutations

Abstract

The homeodomain is a highly conserved DNA-binding motif that is found in numerous transcription factors throughout a large variety of species from yeast to humans. These gene-specific transcription factors play critical roles in development and adult homeostasis, and therefore, any germline mutations associated with these proteins can lead to a number of congenital abnormalities. Although much has been revealed concerning the molecular architecture and the mechanism of homeodomain-DNA interactions, the study of disease-causing mutations can further provide us with instructive information as to the role of particular residues in a conserved mode of action. In this paper, I have compiled the homeodomain missense mutations found in various human diseases and re-examined the functional role of the mutational "hot spot" residues in light of the structures obtained from crystallography. These findings should be useful in understanding the essential components of the homeodomain and in attempts to design agonist or antagonists to modulate their activity and to reverse the effects caused by the mutations.

Fig. 1

Disease-causing missense mutations found in homeodomains and their frequencies. a Individual unique mutations are indicated by stars. Numbers given before each sequence indicate the beginning number of the amino acids, but the residue numbers used in the text follow the conventional numbering system of 1-60 shown top. In the sequence alignment, strictly conserved and highly conserved residues are red and green, respectively. b Mutation frequencies are determined by the number of independent missense mutations found on a particular residue and indicated by a yellow-to-red color scheme. The HNF1α sequence, as a prototype, is shown bottom with the atypical 21 residue insertion between helix 2 and 3

Fig. 2

Mapping of mutations to the homeodomain structure and a detailed structural view of each mutational “hot spot” in HNF1α. a Surface representation of the homeodomain bound to DNA, with mutation sites colored according to the frequencies shown in Fig. 1. b A close-up view of Arg5 and its interactions with DNA. c A close-up view displaying Arg 52 and Arg 53 and their interactions with DNA and neighboring residues. In the majority of homeodomains, there is an additional salt bridge between Arg52 and Glu17 on the first helix to assist the anchoring of the recognition helix at the major groove