The TALE face of Hox proteins in animal evolution

Abstract

Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom.

Keywords: HX; Hox; Meis; Metazoa; PBC; SPIMs; early-branching phyla; patterning.

Figure 1

Origin and early evolution of ANTP- and TALE-class gene families. (A) First evolutionary scenario whereby the Hox/ParaHox family would have derived from a NK member in the Eumetazoan ancestor. (B) Second evolutionary scenario, also named the “ghost loci hypothesis,” whereby the main homeobox gene families (Hox/ParaHox, NK, and Ext-Hox) would have derived from a ProtoANTP cluster of homeobox genes already present in the Last Common Ancestor (LCA) of metazoans. The recent finding of a ParaHox-like gene in Porifera (Fortunato et al., 2014) actually supports the second scenario. Note that only one ParaHox member (symbolized by the absence of red filling) is found in Placozoa [annotated as a Gsx-like: (Schierwater et al., 2008a)] and Porifera [annotated as a Cdx-like: (Fortunato et al., 2014)] and that no Hox or ParaHox gene has been annotated in Ctenophora so far. In comparison, the PBC and Meis families originated earlier in the life tree, with representatives already present in unicellular phyla (Amoebozoa and Filasterea). Graded gray backgrounds highlight Eumetazoa (E), Metazoa (M), Holozoa (H), and Unikonta (U) super phyla. The homeodomain (HD) is indicated in each protein. PBC-A and Meis-A are domains required for the PBC/Meis partnership. Question mark in Choanoflagellata is for incomplete protein sequence of Meis. Animal drawings were taken from Ryan and Baxevanis (2007).

Figure 2

The Hox-TALE interaction network: role of generic (HX motif) and specific PBC interaction motifs (SPIMs). (A) Generic association mode between Hox and TALE proteins. The interaction between Meis and PBC allows the nuclear translocation of PBC. The hexapeptide (HX) motif, present in Hox proteins of all bilaterian lineages, is necessary and sufficient for the generic association mode of the Hox/TALE complex on DNA. (B) Model for the role of SPIMs in specifying patterning functions among Drosophila Hox proteins. The usage of SPIMs allows each Hox protein of the Bithorax complex (BX-C) to adopt different conformation modes with the TALE cofactors and regulate different target genes in vivo (as illustrated by the color code). The placement of SPIMs (highlighted in yellow) in Ultrabithorax (Ubx) and Abdominal-A (Abd-A) reflects the position of the UbdA and TDWM motifs, respectively (Hudry et al., 2012). The placement of the SPIM in Abdominal-B (Abd-B) is speculative.

Figure 3

Cnidarian and bilaterian Hox/TALE networks display similar interaction properties. Ancestral Hox/TALE networks were strictly relying on the HX motif. The apparition of SPIMs in bilaterian and cnidarian lineages allowed Hox proteins to diversify their interaction modes with the TALE partners. Pictures depict in vivo interaction between Hox and PBC proteins in a live Drosophila (right) or Nematostella embryo, as described in Hudry et al. (2011, 2014). Compared to Drosophila, the usage of SPIMs in Nematostella Hox proteins is strictly dependent on the presence of Meis (Hudry et al., 2014). The absence of identical SPIMs between bilaterian and cnidarian Hox proteins suggests that these motifs emerged independently in these two groups (see also Figure 4).

Figure 4

Two evolutionary scenarios for the origin and early evolution of Hox-TALE interaction properties. (A) In the first scenario, the HX motif arose in the ProtoANTP gene of the metazoan LCA. There were multiple secondary losses in the Hox/ParaHox (sl; highlighted in blue) and other families (not indicated) in ctenophores, porifers, placozoans and cnidarians. (B) In the second scenario, the HX motif appeared independently several times during evolution, acquired in the Hox/ParaHox (red arrow), and NK (Msx, orange arrow) families of the last common ancestor of Cnidaria and Bilateria (CBA), or in Ext-Hox members (as exemplified with En, yellow arrow) of the bilaterian ancestor. The absence of the HX motif in Hox/ParaHox members of several cnidarian species indicates secondary lost events (highlighted in blue; see also Table 1). In both scenarios, the HX motif served as a molecular template for diversifying TALE interaction properties only in the Hox/ParaHox family. This was achieved by the emergence of SPIMs. These motifs were independently acquired (highlighted in red) in Bilateria and Cnidaria, coinciding with strong morphological radiation in these two phyla.

Figure 5

SPIMs as molecular markers of a Hox/TALE patterning system during animal evolution. The acquisition of SPIMs in Cnidaria (Nematostella) and Bilateria (Drosophila, mammals) allowed Hox proteins to diversify their interaction modes with the TALE partners. This molecular diversification was essential for providing differential activities to Hox proteins along the longitudinal axis. Illustrative examples are provided along the anterior-posterior axis of the Drosophila embryo or along the directive axis of the Nematostella embryo. Anterior (ant), central (cent), and posterior (post) Hox proteins are depicted by a different color. In Placozoa and Porifera, ParaHox-like members are present but these proteins do not contain any HX motif. Along the same line, placozoan and poriferan PBC and Meis representatives lack the PBC-A and MEIS-A domains (see Figure 1) and thus cannot interact together. As a consequence, TALE interaction networks do likely not exist in those two phyla. We postulate that Hox/ParaHox transcription factors were initially dedicated to cell proliferation/cell differentiation with no patterning function, whereas Hox/TALE interactions co-evolved with patterning functions.