Hox protein: Difference between revisions

[[Image:Cell.jpg|thumb|right|300px|Figure 2: Hox proteins require a cofactor to achieve high binding specificity in order to execute their distinct functions in developing various parts of the fly embryo. Elsevier/Cell Press has provided permission for usage of this figure<ref name="slattery">Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 2011;147(6):1270-82. [http://www.ncbi.nlm.nih.gov/pubmed/22153072 PMID:22153072]</ref>.]]

Hox proteins are transcription factors that play a key role in the '''embryonic development''' across species by activating and repressing genes. In ''Drosophila,'' eight Hox proteins are responsible for the development of different body segments of the fly, such as its antennae, wings, or legs. Hox proteins execute their distinct functions through binding to similar but different in vivo binding sites<ref>Mann RS, Lelli KM, Joshi R. Hox specificity unique roles for cofactors and collaborators. Curr Top Dev Biol. 2009;88:63-101. [http://www.ncbi.nlm.nih.gov/pubmed/19651302 PMID:19651302]</ref>. This page discusses molecular mechanisms through which Hox proteins recognize their DNA targets with very high binding specificity. <br/>

[[Image:Joshi-etal-Figure7.jpg‎ |thumb|left|300px|Figure 4: Expression patterns of Scr in presence of Scr specific site (left panel) vs. Hox consensus site (right panel). Elsevier/Cell Press has provided permission for usage of this figure<ref name="joshi"/>.]]

In vitro binding studies have shown that His-12 and Arg-3 mutations have a large effect when exposed to the Scr specific site, whereas the effect is small when exposed to a Hox consensus site. The biological importance of both side chains becomes apparent in ''in vivo'' experiments. Upon mutations of His-12 and Arg-3 to alanine, Scr expression in a fly embryo is dramatically affected (Figure 4). In comparison to  wild type Scr (A) and based on ectopic expression (B), there is only residual expression detected in  

the thorax region of the double mutant when the Scr specific site is tested (C), whereas there is no apparent effect on expression in the presence of a Hox consensus site (D-F).<br/>

[[Image:Cell2007-Fig4.jpg‎ |thumb|left|300px|Figure 6: Comparison of DNA shape of Scr specific in vivo site (left panel) vs. Hox consensus site (right panel). Elsevier/Cell Press has provided permission for usage of this figure<ref name="joshi"/>.]]

Based on the comparison of the two crystal structures of a Scr-Exd-DNA ternary complexes (Figure 6), it was found that three N-terminal residues contact the minor groove of the Scr specific site ''fkh250'' (A) compared to only Arg5 binding the Hox consensus site ''fkh250con'' (B). In their protein-bound states, the shapes of both sites are distinct (dark gray, concave; green, convex surfaces). The distinct shapes of the two DNA binding sites, shown as minor groove width in the crystal structures of the complexes (blue plots), are already present when the protein is not bound to the DNA, with two minima in ''fkh250'' (C) vs. one minimum in ''fkh250con'' (D), as inferred by Monte Carlo simulations (green plots). Minor groove width (blue plots) and electrostatic potential (red plots) correlate and form two binding pockets in ''fkh250'' (E) and only a binding site for Arg5 in ''fkh250con'' (F).<br/>

[[Image:Slattery-etal-Figure6.jpg‎ |thumb|right|300px|Figure 7:  DNA shape analysis of >650,000 sites derived from SELEX-seq experiments. Elsevier/Cell Press has provided permission for usage of this figure<ref name="slattery"/>.]]

Based on SELEX-seq data and a method for high-throughput prediction of DNA shape, the same pattern of two minima in minor groove width (A) was predicted for the binding sites of all anterior Hox proteins vs. a single minimum (A) for all posterior Hox proteins (dark green for narrow groove, white for wide groove). Frames highlight the regions that correspond to the minima in Figure 6. Differences in minor groove width between binding sites can be visualized in a Euclidean distance dendrogram, which forms two branches representing anterior and posterior Hox proteins (B). The differences between both groups are significant as shown by Pearson correlation (C). Remarkably, using DNA shape of their selected binding sites the eight ''Drosophila'' Hox proteins order according to their collinearity. This result, thus, indicates how Hox genes have likely differentiated throughout evolution.<br/>