Homeodomains

Homeodomain proteins are involved in the development of many eucaryotic organisms... 

Eucaryotes have many more genes and a broader range of specific transcription factors than procaryotes and gene expression is regulated by using sets of these factors in a combinatorial way. Eucaryotes have found several different solutions to the problem of producing a three-dimensional scaffold that allows a protein to interact specifically with DNA. In the next chapter we shall discuss some of the solutions that have no counterpart in procaryotes. However, the procaryotic helix-turn-helix solution to this problem (see Chapter 8) is also exploited in eucaryotes, in homeodomain proteins and some other families of transcription factors. 

Homeoboxes code for homeodomains, sequences of 60 amino acids that function as the DNA-binding regions of transcription factors. Each homeo-box gene in Drosophila is expressed only in its own characteristic subset of embryonic cells, and almost every embryonic cell contains a unique combination of homeodomain proteins. 

Monomers of homeodomain proteins bind to DNA through a helix-turn-helix motif... 

The homeodomain frequently binds to DNA as a monomer, in contrast to procaryotic DNA-binding proteins containing tbe belix-turn-helix motif, which usually bind as dimers. In vitro tbe homeodomain binds specifically to... 

Figure 9.8 Schematic diagram of the three-dimensional structure of the Antennapedia homeodomain. The structure is built up from three a helices connected by short loops. Helices 2 and 3 form a helix-turn-hellx motif (blue and red) similar to those in procaryotic DNA-binding proteins. (Adapted from Y.Q. Qian et al.. Cell 59 573-580, 1989.)...

Fi re 9.9 Comparison of the hellx-tum-helix motifs in homeodomains (a) and X repressor (b). The recognition helix (red) of the homeodomain is longer than in the procaryotic repressor motif. In addition the first helix of the homeodomain [(green in (a)] is oriented differently. 

Residues 3, 5, 6, and 8 in the N-terminal arm lie in the minor groove and form contacts with either the edge of the bases or with the DNA backbone. Almost all homeodomains contain four conserved residues, Asn 51, Arg 53, Trp 48 and Phe 49, in the middle of the long recognition helix. The first two conserved polar residues interact with DNA. The second two are part of the hydrophobic core of the homeodomain, and are important for the accurate positioning of the recognition helix and the N-terminal arm with respect to... 

Figure 9.10 Schematic diagrams illustrating the complex between DNA (orange) and one monomer of the homeodomain. The recognition helix (red) binds in the major groove of DNA and provides the sequence-specific interactions with bases in the DNA. The N-terminus (green) binds in the minor groove on the opposite side of the DNA molecule and arginine side chains make nonspecific interactions with the phosphate groups of the DNA. (Adapted from C.R. Kissinger et al Cell 63 579-590, 1990.)...

Figure 9.11 Amino acid sequences of homeodomains from four differenf franscription factors Anfp is from fhe Antennapedia gene in the fruitfly Drosophila, a2 is from the yeast Mat o2 gene, eng is from fhe engrailed gene in Drosophila and POU is from fhe POU homeodomain in the mammalian gene Oct-1. Residues colored green form the hydrophobic core of the homeodomain, blue form nonspecific interactions with the DNA backbone and red form contacts with the edges of the DNA bases.

In vivo specificity of homeodomain transcription factors depends on interactions with other proteins... 

Figure 9.12 Schematic diagram of the structure of the heterodimeric yeast transcription factor Mat a2-Mat al bound to DNA. Both Mat o2 and Mat al are homeodomains containing the helix-turn-helix motif. The first helix in this motif is colored blue and the second, the recognition helix, is red. (a) The assumed structure of the Mat al homeodomain in the absence of DNA, based on Its sequence similarity to other homeodomains of known structure, (b) The structure of the Mat o2 homeodomain. The C-terminal tail (dotted) is flexible in the monomer and has no defined structure, (c) The structure of the Mat a 1-Mat a2-DNA complex. The C-terminal domain of Mat a2 (yellow) folds into an a helix (4) in the complex and interacts with the first two helices of Mat a2, to form a heterodimer that binds to DNA. (Adapted from B.J. Andrews and M.S. Donoviel, Science 270 251-253, 1995.)...

How is the binding specificity of the heterodimer achieved compared with the specificity of Mat a2 alone The crystal structure rules out the simple model that the contacts made between the Mat a2 homeodomain and DNA are altered as a result of heterodimerization. The contacts between the Mat o2 homeodomain and DNA in the heterodimer complex are virtually indistinguishable from those seen in the structure of the Mat o2 monomer bound to DNA. However, there are at least two significant factors that may account for the increased specificity of the heterodimer. First, the Mat al homeodomain makes significant contacts with the DNA, and the heterodimeric complex will therefore bind more tightly to sites that provide the contacts required by both partners. Second, site-directed mutagenesis experiments have shown that the protein-protein interactions involving the... 

Figure 9.13 The DNA-binding region of the protein Oct-1, the POU region (green), comprises two domains, the POU-specific domain (dark green) and the POU homeodomain (light green) joined by a linker region (blue). These two domains bind to DNA in a tandem arrangement.

Figure 9.14 The two domains of the POU region bind in tandem on opposite sides of the DNA double helix. Both the POU-specific domain and the POU homeodomain have a helix-turn-helix motif (blue and red) which binds to DNA with their recognition helices (red) in the major groove. The linker region that joins these domains is partly disordered. (Adapted from J.D. Klemm et al.. Cell 77 21-32, 1994.)...

Both domains of the POU region bind to DNA by the usual combination of non specific binding to the DNA backbone and specific binding to the bases. The contacts between the homeodomain and DNA are similar to those of the engrailed homeodomain (compare Figures 9.10b and 9.15a) and the... 

Much remains to be learnt about the function of homeodomains in vivo... 

Kissinger, C.R., et al. Crystal structure of an engrailed homeodomain DNA complex at 2.8 A resolution a framework for understanding homeodomain-DNA interactions. Cell 63 579-590, 1990. 

Wilson, D.S., et al. Crystal structure of a paired (PAX) class cooperative homeodomain dimer on DNA. Cell 82 709-719, 1995. 

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