Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein

Hox proteins are among the most intensively studied transcription factors and represent key factors in establishing morphological differences along the anterior–posterior axis of animals. They are generally regarded as highly conserved in function, a view predominantly based on experiments comparing a few (anterior) Hox proteins. However, the extent to which central or abdominal Hox proteins share conserved functions and sequence signatures remains largely unexplored. To shed light on the functional divergence of the central Hox proteins, we present an easy to use resource aimed at predicting the functional similarities of central Hox proteins using sequence elements known to be relevant to Hox protein functions. We provide this resource both as a stand-alone download, including all information, as well as via a simplified web-interface that facilitates an accurate and fine-tuned annotation of novel Hox sequences. The method used in the manuscript is, so far, the only published sequence-based method capable of differentiating between the functionally distinct central Hox proteins with near-identical homeodomains (such as the Drosophila Antp, Ubx and Abd-A Hox proteins). In this manuscript, a pairwise-sequence-similarity based approach (using the bioinformatics tool CLANS) is used to analyze all available central Hox protein sequences. The results are combined with a large-scale species phylogeny to depict the presence/absence of central Hox sequence-types across the bilaterian lineage. The obtained pattern of distribution of the Hox sequence-types throughout the species tree enables us to infer at which branching point a specific type of central Hox protein was present. Based on the Hox sequences currently available in public databases, seven sequence-similarity groups could be identified for the central Hox proteins, two of which have never been described before (Echi/Hemi7 and Echi/Hemi8). Our work also shows, for the first time, that Antp/Hox7-like sequences are present throughout all bilaterian clades and that all other central Hox protein groups are specific to sub-lineages in the protostome or deuterostome branches only.