elife01939.xml

<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d1 20130915//EN"  "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1d1" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="hwp">eLife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">01939</article-id><article-id pub-id-type="doi">10.7554/eLife.01939</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research article</subject></subj-group><subj-group subj-group-type="heading"><subject>Developmental biology and stem cells</subject></subj-group><subj-group subj-group-type="heading"><subject>Genomics and evolutionary biology</subject></subj-group></article-categories><title-group><article-title>Molecular insights into the origin of the Hox-TALE patterning system</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" id="author-6558"><name><surname>Hudry</surname><given-names>Bruno</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="other" rid="par-3"/><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-6559"><name><surname>Thomas-Chollier</surname><given-names>Morgane</given-names></name><xref ref-type="aff" rid="aff2"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-6560"><name><surname>Volovik</surname><given-names>Yael</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-9482"><name><surname>Duffraisse</surname><given-names>Marilyne</given-names></name><xref ref-type="aff" rid="aff4"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-9483"><name><surname>Dard</surname><given-names>Amélie</given-names></name><xref ref-type="aff" rid="aff4"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-6561"><name><surname>Frank</surname><given-names>Dale</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-6562"><name><surname>Technau</surname><given-names>Ulrich</given-names></name><xref ref-type="aff" rid="aff5"/><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-6440"><name><surname>Merabet</surname><given-names>Samir</given-names></name><xref ref-type="aff" rid="aff4"/><xref ref-type="corresp" rid="cor2">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><institution content-type="dept">MRC Clinical Sciences Centre, Faculty of Medicine</institution>, <institution>Imperial College London</institution>, <addr-line><named-content content-type="city">London</named-content></addr-line>, <country>United Kingdom</country></aff><aff id="aff2"><institution content-type="dept">Unité Mixte de Recherche (UMR) 8197, INSERM U1024, Institut de Biologie de l’ENS (IBENS)</institution>, <institution>Ecole Normale Supérieure (ENS), Centre National de Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Scientifique (INSERM)</institution>, <addr-line><named-content content-type="city">Paris</named-content></addr-line>, <country>France</country></aff><aff id="aff3"><institution content-type="dept">Department of Biochemistry, The Rappaport Family Institute for Research in the Medical Sciences, Faculty of Medicine, Technion</institution>, <institution>Israel Institute of Technology</institution>, <addr-line><named-content content-type="city">Haifa</named-content></addr-line>, <country>Israel</country></aff><aff id="aff4"><institution content-type="dept">Unité Mixte de Recherche (UMR) 5242, Institut de Génomique Fonctionnelle de Lyon (IGFL)</institution>, <institution>Ecole Normale Supérieure (ENS) de Lyon, Centre National de Recherche Scientifique (CNRS)</institution>, <addr-line><named-content content-type="city">Lyon</named-content></addr-line>, <country>France</country></aff><aff id="aff5"><institution content-type="dept">Department für Molekulare Evolution und Entwicklung</institution>, <institution>University of Vienna</institution>, <addr-line><named-content content-type="city">Vienna</named-content></addr-line>, <country>Austria</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Tautz</surname><given-names>Diethard</given-names></name><role>Reviewing editor</role><aff><institution>Max Planck Institute for Evolutionary Biology</institution>, <country>Germany</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>petithudry@gmail.com</email> (BH);</corresp><corresp id="cor2"><label>*</label>For correspondence: <email>samir.merabet@ens-lyon.fr</email> (SM)</corresp></author-notes><pub-date date-type="pub" publication-format="electronic"><day>18</day><month>03</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>3</volume><elocation-id>e01939</elocation-id><history><date date-type="received"><day>09</day><month>12</month><year>2013</year></date><date date-type="accepted"><day>01</day><month>02</month><year>2014</year></date></history><permissions><copyright-statement>© 2014, Hudry et al</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Hudry et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife01939.pdf"/><related-article ext-link-type="doi" id="ra1" related-article-type="commentary" xlink:href="10.7554/eLife.02515"/><abstract><object-id pub-id-type="doi">10.7554/eLife.01939.001</object-id><p>Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.001">http://dx.doi.org/10.7554/eLife.01939.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><object-id pub-id-type="doi">10.7554/eLife.01939.002</object-id><title>eLife digest</title><p>Any animal with a body that is symmetric about an imaginary line that runs from its head to its tail is known as a bilaterian. Humans and most animals are bilateral, whereas jellyfish and starfish are not. Bilateral symmetry can take many forms—as demonstrated by the differences between flies, frogs and humans—but all bilaterians express many of the same genes during development.</p><p>One of these groups of genes is known as the Hox family. The expression of specific Hox genes at specific times instructs cells in the developing embryo to adopt different fates according to their position along the anterior–posterior (head to tail) axis. The patterning function of Hox genes relies on the presence of two additional cofactors that belong to the so-called TALE family. Although both Hox and TALE proteins were present early on during animal evolution, it is unclear how and when the interactions between them first began to generate symmetrical body plans.</p><p>Now, Hudry et al. have provided insights into the origin of the Hox-TALE network by analysing the expression and molecular properties of Hox and TALE proteins from various multicellular and unicellular organisms. These experiments revealed that Hox and TALE proteins of the sea anemone <italic>Nematostella</italic>, which belongs to a group of animals called cnidarians that have radial rather than bilateral symmetry, interact with one another in a similar manner to the interactions seen in bilaterians.</p><p>Hudry et al. then showed that two <italic>Nematostella</italic> Hox genes were able to substitute for their bilaterian equivalents in fruit flies, and that a <italic>Nematostella</italic> TALE gene was able to take over neuronal functions of its equivalent in <italic>Xenopus</italic> frogs. This striking conservation of function between species suggests that Hox and TALE genes were already working together in the common ancestor of all bilaterian and cnidarian animals.</p><p>By contrast, TALE members from a unicellular amoeba were unable to interact with Hox proteins, suggesting that Hox–TALE interactions first emerged in multicellular animals. In addition to increasing our knowledge of highly conserved Hox signalling, these data provide insight into the molecular mechanisms that gave rise to the symmetrical body plan that has been adopted, and adapted, by the majority of animals since.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.002">http://dx.doi.org/10.7554/eLife.01939.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author keywords</title><kwd>Hox</kwd><kwd>TALE</kwd><kwd>evolution</kwd><kwd>network</kwd><kwd>transcription factors</kwd><kwd><italic>Nematostella vectensis</italic></kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd><italic>D. melanogaster</italic></kwd><kwd>other</kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution>Association pour la Recherche contre le Cancer</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Hudry</surname><given-names>Bruno</given-names></name><name><surname>Thomas-Chollier</surname><given-names>Morgane</given-names></name><name><surname>Volovik</surname><given-names>Yael</given-names></name><name><surname>Duffraisse</surname><given-names>Marilyne</given-names></name><name><surname>Dard</surname><given-names>Amélie</given-names></name><name><surname>Frank</surname><given-names>Dale</given-names></name><name><surname>Technau</surname><given-names>Ulrich</given-names></name><name><surname>Merabet</surname><given-names>Samir</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution>Fondation pour la Recheche Medicale</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Hudry</surname><given-names>Bruno</given-names></name><name><surname>Thomas-Chollier</surname><given-names>Morgane</given-names></name><name><surname>Volovik</surname><given-names>Yael</given-names></name><name><surname>Duffraisse</surname><given-names>Marilyne</given-names></name><name><surname>Dard</surname><given-names>Amélie</given-names></name><name><surname>Frank</surname><given-names>Dale</given-names></name><name><surname>Technau</surname><given-names>Ulrich</given-names></name><name><surname>Merabet</surname><given-names>Samir</given-names></name></principal-award-recipient></award-group><award-group id="par-3"><funding-source><institution-wrap><institution>EMBO short term fellow</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Hudry</surname><given-names>Bruno</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>Interactions between Hox and TALE genes, which generate bilaterally symmetrical body plans, originated in early multicellular animals.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>‘What is an animal?’ In 1993, Slack et al. proposed to define an animal by the zootype (<xref ref-type="bibr" rid="bib62">Slack et al., 1993</xref>), a concept illustrating the strong conservation of embryonic expression profiles of developmental genes observed in different bilaterian phyla at that time. Since then, it was found that developmental genes could also display highly dissimilar expression patterns or even be absent in non-bilaterian lineages, showing that the genetic mechanisms underlying embryonic development are not universal.</p><p>One major class of developmental genes that was historically considered as highly conserved in the animal kingdom is the Hox genes. Hox genes are expressed along the anteroposterior axis of all bilaterian animals, providing positional information during embryogenesis. Given their important patterning roles, Hox genes are thought to have strongly contributed to morphological diversification of bilaterian organisms during evolution. Accordingly, numerous examples have shown that modifications in Hox genes number, expression, and/or activity could correlate to morphological variations across bilaterian lineages (<xref ref-type="bibr" rid="bib26">Heffer and Pick, 2013</xref>).</p><p>The role of Hox genes suffers more ambiguity outside Bilateria, and in particular in the sister Cnidaria group. Cnidarians do contain Hox genes and have undergone a wide range of morphological radiation during evolution. However, Hox genes have neither a clear collinear nor conserved expression profile along the primary (oral–aboral) axis of the planula larva among different cnidarian lineages (<xref ref-type="bibr" rid="bib18">Finnerty et al., 2004</xref>; <xref ref-type="bibr" rid="bib34">Kamm et al., 2006</xref>), which renders their orthology status difficult to assign (specially for posterior/non-anterior cnidarian Hox genes). A role of Hox genes in axis patterning was proposed in the hydrozoan <italic>Eleutheria dichotoma</italic> (<xref ref-type="bibr" rid="bib32">Jakob and Schierwater, 2007</xref>), but these results are limited by the fact that functional analyses were performed in medusa, a particular developmental stage that is not shared by all cnidarian species. The role of cnidarian Hox genes during early larval stages is, however, currently unclear.</p><p>Interestingly, Cnidaria is the only non-bilaterian phylum, which has a bona fide Hox repertoire, whereas others, including ctenophores, sponges, and placozoans, lack Hox genes (<xref ref-type="fig" rid="fig1">Figure 1</xref>). This raises the important question of how the Hox gene family acquired its crucial axial patterning functions during metazoan evolution. In Bilateria, Hox patterning functions rely on the presence of the PBC and Meis proteins, which are also present in non-bilaterian phyla (<xref ref-type="fig" rid="fig1">Figure 1</xref>). We thus assessed whether a Hox/PBC/Meis network could exist outside Bilateria, and if so whether or not it would rely on identical molecular rules as observed in Bilateria.<fig id="fig1" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.003</object-id><label>Figure 1.</label><caption><title>Phylogeny of Hox (ANTP superclass) and PBC/Meis (TALE superclass) proteins across eukaryote evolution.</title><p>Protein motifs required for Hox/PBC/Meis network are indicated when present: homeodomain (HD), hexapeptide (HX), PBC-A, and MEIS-A. Absence of the member in a given group is considered as resulting from a secondary loss (sl), when the ortholog is present more ancestrally. A question mark is indicated for Meis of <italic>Monosiga brevicollis</italic> because of incomplete sequence. The protein indicated in Placozoa is not coloured in blue since it is not a true Hox protein (see main text for details). Examples are provided for a representative species of each group. Members of PBC and Meis classes are called Pbx or Extradenticle (Exd) and Meis or Homothorax (Hth), respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.003">http://dx.doi.org/10.7554/eLife.01939.003</ext-link></p></caption><graphic xlink:href="elife01939f001"/></fig></p><p>Hox and PBC/Meis proteins belong to the ANTP (Antennapedia) and TALE (Three amino acids loop extension) class of homeodomain (HD)-containing TFs, respectively (<xref ref-type="bibr" rid="bib55">Saina et al., 2009</xref>). The Hox/PBC/Meis network relies on interactions between PBC and Meis proteins on one side, and on interactions between Hox and PBC proteins on the other side (<xref ref-type="bibr" rid="bib41">Mann et al., 2009</xref>). Some posterior vertebrate Hox members do form dimeric complexes with Meis (<xref ref-type="bibr" rid="bib60">Shen et al., 1997</xref>; <xref ref-type="bibr" rid="bib67">Williams et al., 2005</xref>), but these interactions constitute a vertebrate innovation rather than a general rule in Bilateria. Interactions between PBC and Meis occur through conserved regions localized upstream of the HD of both proteins (called PBC-A and MEIS-A domains) and which are thought to derive from a common ancestor domain (<xref ref-type="bibr" rid="bib6">Burglin, 1998</xref>). These interactions allow the nuclear translocation and stability of PBC (<xref ref-type="bibr" rid="bib1">Abu-Shaar et al., 1999</xref>). Interactions between Hox and PBC involve a short conserved motif in Hox proteins, called the hexapeptide (HX), which folds within the hydrophobic pocket formed in part by the extra-three residues of the HD of PBC (<xref ref-type="bibr" rid="bib47">Merabet et al., 2009</xref>). This motif contains a conserved core sequence of four residues in all but AbdB-group Hox proteins, which retain a single tryptophan residue. Additional specific signatures can also be found in the HX of some paralog groups (<xref ref-type="bibr" rid="bib47">Merabet et al., 2009</xref>). Recent data showed that Hox proteins could also interact with PBC partners through other more specific motifs. These alternative interaction modes can be induced by the DNA-binding of the Meis partner, eventually leading to different three-dimensional conformations that could be important for paralog-specific functions (<xref ref-type="bibr" rid="bib20">Galant et al., 2002</xref>; <xref ref-type="bibr" rid="bib46">Merabet et al., 2007</xref>; <xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>).</p><p>PBC and Meis representatives are found from unicellular Amoebozoa and Filasterea groups to metazoan lineages including Ctenophora and Placozoa (<xref ref-type="fig" rid="fig1">Figure 1</xref>). Sequence analysis shows that only one PBC or Meis representative is present, or that the protein does not contain the PBC-A or MEIS-A interaction domain in most of these lineages (<xref ref-type="fig" rid="fig1">Figure 1</xref>, <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2—figure supplements 1 and 2</xref>). Interestingly, all protein features required for PBC/Meis partnership appeared concomitantly with the presence of Hox or Hox-like proteins in Metazoa (<xref ref-type="fig" rid="fig1">Figure 1</xref>). Of note, the representative species of Placozoa, <italic>Trichoplax adhaerens</italic> (<italic>Ta</italic>), contains a protein that was classified as a ProtoHox (<xref ref-type="bibr" rid="bib58">Schierwater and Kuhn, 1998</xref>) or ParaHox (<xref ref-type="bibr" rid="bib45">Mendivil Ramos et al., 2012</xref>) member (<xref ref-type="fig" rid="fig1">Figure 1</xref>). However, the absence of any HX motif (<xref ref-type="bibr" rid="bib58">Schierwater and Kuhn, 1998</xref>) suggests that this protein could not interact with PBC/Meis, which is confirmed later (see last section of ‘Results’).</p><p>Protein sequence analysis indicates that a Hox/PBC/Meis network could first be present in Cnidaria. To test this hypothesis, we dissected the molecular properties underlying the formation of the Hox/PBC/Meis interaction network of the sea anemone <italic>Nematostella vectensis</italic> (<italic>Nv</italic>), a cnidarian species exhibiting an internal symmetry organized along oral–aboral (primary) and directive (secondary) body axes (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). This analysis was performed in vitro and in vivo and completed by heterologous functional assays in vertebrate and invertebrate species. Since other members of the ANTP superclass are described to interact with PBC in Bilateria, we also searched for the molecular mechanisms that allowed the emergence of the Hox–TALE network during evolution of homeobox gene families.<fig-group><fig id="fig2" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.004</object-id><label>Figure 2.</label><caption><title>Hox and TALE members are co-expressed in the endoderm of the Nematostella embryo.</title><p>(<bold>A</bold>) Genomic organisation of Hox genes in <italic>Nematostella vectensis</italic> (<italic>Nv</italic>) and <italic>Drosophila melanogaster</italic> (<italic>Dm</italic>), two representative species of Cnidaria and Bilateria, respectively. Embryos at the planula stage are schematized; A–P: anterior–posterior; D–V: dorsal–ventral; A–O: aboral–oral; Di: directive axis. The Nematostella embryo is oriented according to recent findings (<xref ref-type="bibr" rid="bib61">Sinigaglia et al., 2013</xref>). The nomenclature is calqued on (<xref ref-type="bibr" rid="bib10">Chourrout et al., 2006</xref>) to avoid confusions with bilaterian Hox paralogs: <italic>NvHoxC</italic> (<italic>antHox7</italic>), <italic>NvHoxDa</italic> (<italic>antHox8</italic>), <italic>NvHoxDb</italic> (<italic>antHox8a</italic>), <italic>NvHoxA</italic> (<italic>antHox6</italic>), <italic>NvHoxB</italic> (<italic>antHox6a</italic>), <italic>NvHoxE</italic> (<italic>antHox1a</italic>), <italic>NvHoxF</italic> (<italic>antHox1</italic>). The two Nematostella Hox genes under study, <italic>NvHoxB</italic> and <italic>NvHoxE</italic>, are highlighted in blue and red respectively. Note that the same colour code is used in other figures. (<bold>B</bold>) Sequence identity between Nematostella and Drosophila proteins. <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE are compared to Labial (Lab) and Ultrabithorax (Ubx) respectively. The percentage of identity is represented by a grayscale gradient. Conserved domains in bilaterian TALE proteins are indicated (<bold>A</bold>, <bold>B</bold>, <bold>C</bold>, <bold>D</bold>). HX: hexapeptide. HD: homeodomain. See also <xref ref-type="fig" rid="fig2s1 fig2s2 fig2s3 fig2s4">Figure 2—figure supplements 1–4</xref>. (<bold>C</bold>) In situ hybridization of <italic>NvPbx</italic>, <italic>NvMeis</italic>, <italic>NvHoxB</italic> and <italic>NvHoxE</italic> in a three-day-old Nematostella planula. These four genes are expressed in the endoderm (en), as illustrated in (<bold>D</bold>). Ec: ectoderm. <italic>NvPbx</italic> and <italic>NvMeis</italic> are illustrated in grey and black, respectively. This colour code is used in other figures.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.004">http://dx.doi.org/10.7554/eLife.01939.004</ext-link></p></caption><graphic xlink:href="elife01939f002"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.005</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Protein sequence alignment of PBC members from representative species of Unikonta.</title><p>Regions encompassing the PBC-A domain and homeodomain (HD) are highlighted in grey and yellow respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.005">http://dx.doi.org/10.7554/eLife.01939.005</ext-link></p></caption><graphic xlink:href="elife01939fs001"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.006</object-id><label>Figure 2—figure supplement 2.</label><caption><title>Protein sequence alignment of Meis members from representative species of Unikonta.</title><p>Regions encompassing the MEIS-A domain and homeodomain (HD) are highlighted in grey and yellow respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.006">http://dx.doi.org/10.7554/eLife.01939.006</ext-link></p></caption><graphic xlink:href="elife01939fs002"/></fig><fig id="fig2s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.007</object-id><label>Figure 2—figure supplement 3.</label><caption><title>Protein sequence alignment between NvHoxB and the Labial (Lab) protein from <italic>Drosophila melanogaster</italic>.</title><p>Homeodomain and hexapeptide regions are highlighted in blue and red respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.007">http://dx.doi.org/10.7554/eLife.01939.007</ext-link></p></caption><graphic xlink:href="elife01939fs003"/></fig><fig id="fig2s4" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.008</object-id><label>Figure 2—figure supplement 4.</label><caption><title>Protein sequence alignment between NvHoxE and the Ultrabithorax (Ubx) or AbdominalB (AbdB) protein from <italic>Drosophila melanogaster</italic>.</title><p>Homeodomain and hexapeptide regions are highlighted in blue and red respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.008">http://dx.doi.org/10.7554/eLife.01939.008</ext-link></p></caption><graphic xlink:href="elife01939fs004"/></fig></fig-group></p><p>Our results show that Hox and TALE proteins from <italic>Nematostella</italic> form interaction networks and perform similar functions to their bilaterian counterparts. Although these networks rely on intricate molecular properties, they originated from an ancestral generic mode of interaction that was kept in other homebox gene families. Overall our study describes how the molecular cues underlying the Hox–TALE patterning system in Bilateria was established stepwise during eukaryote evolution.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title>Hox and TALE members are co-expressed and form protein complexes in the <italic>Nematostella</italic> embryo</title><p>The <italic>Nematostella</italic> genome contains seven Hox genes and one representative of the PBC (<italic>NvPbx</italic>) or Meis (<italic>NvMeis</italic>) class (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis proteins show a high level of sequence conservation with their bilaterian counterparts, especially in the regions encompassing the HD, PBC-A, and Meis-A domains (<xref ref-type="fig" rid="fig2">Figure 2B</xref>, <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2—figure supplements 1 and 2</xref>). In contrast, sequence similarity between cnidarian Hox proteins and their bilaterian homologs is restricted to the region encompassing the HD, as exemplified for <italic>Nv</italic>HoxB (<xref ref-type="fig" rid="fig2">Figure 2B</xref>, <xref ref-type="fig" rid="fig2s3">Figure 2—figure supplement 3</xref>) and <italic>Nv</italic>HoxE (<xref ref-type="fig" rid="fig2">Figure 2B</xref>, <xref ref-type="fig" rid="fig2s4">Figure 2—figure supplement 4</xref>). Some <italic>Nv</italic>Hox proteins do also contain a HX motif, as noticed in <italic>Nv</italic>HoxB or <italic>Nv</italic>HoxE (<xref ref-type="fig" rid="fig2">Figure 2B</xref>, <xref ref-type="fig" rid="fig2s3 fig2s4">Figure 2—figure supplements 3 and 4</xref>). The HX of <italic>Nv</italic>HoxE is more divergent, corresponding to a single tryptophan residue as found in bilaterian Hox posterior paralog groups. Still, the identity of <italic>NvHoxE</italic> (as well as those of <italic>NvHoxF</italic>) remains controversial, being classified as a cnidarian-specific (<xref ref-type="bibr" rid="bib10">Chourrout et al., 2006</xref>; <xref ref-type="bibr" rid="bib50">Ryan et al., 2006</xref>), posterior (<xref ref-type="bibr" rid="bib21">Gauchat et al., 2000</xref>; <xref ref-type="bibr" rid="bib51">Ryan et al., 2007</xref>), or central Hox gene (<xref ref-type="bibr" rid="bib65">Thomas-Chollier et al., 2010</xref>). This is not the case for <italic>NvHoxC</italic>, <italic>NvHoxDa</italic>, <italic>NvHoxDb</italic>, <italic>NvHoxA</italic> and <italic>NvHoxB</italic>, which are unambiguously assigned as anterior Hox genes (<xref ref-type="bibr" rid="bib10">Chourrout et al., 2006</xref>; <xref ref-type="bibr" rid="bib50">Ryan et al., 2006</xref>, <xref ref-type="bibr" rid="bib51">2007</xref>; <xref ref-type="bibr" rid="bib65">Thomas-Chollier et al., 2010</xref>; <xref ref-type="fig" rid="fig2">Figure 2A</xref>).</p><p>To first verify that Hox, PBC, and Meis products from <italic>Nematostella</italic> could form an interaction network in vivo, we performed in situ hybridization experiments using <italic>NvPbx</italic> (<xref ref-type="bibr" rid="bib43">Matus et al., 2006</xref>) and <italic>NvMeis</italic> probes. Results showed that the transcripts of these two genes are co-expressed in the entire endoderm of the larva (<xref ref-type="fig" rid="fig2">Figure 2C–D</xref>). Interestingly, several Hox genes were previously described to be expressed in staggered domains along the directive axis in the same tissue (<xref ref-type="bibr" rid="bib18">Finnerty et al., 2004</xref>; <xref ref-type="bibr" rid="bib42">Matus et al., 2006</xref>; <xref ref-type="bibr" rid="bib51">Ryan et al., 2007</xref>), which was here confirmed for <italic>NvHoxB</italic> and <italic>NvHoxE</italic> (<xref ref-type="fig" rid="fig2">Figure 2C–D</xref>).</p><p>The relationship between <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis was then analysed by expressing a tagged version of <italic>Nv</italic>Pbx, alone or with <italic>Nv</italic>Meis. Analyses were performed in a 24-hr-old embryo, at a stage when endogenous <italic>NvMeis</italic> is not yet expressed. We observed that the nuclear accumulation of mCherry-<italic>Nv</italic>Pbx fusion protein is contingent upon co-injection with <italic>Nv</italic>Meis (<xref ref-type="fig" rid="fig3">Figure 3A</xref>). Thus, <italic>Nv</italic>Meis is able to stabilize <italic>Nv</italic>Pbx, eventually triggering its nuclear accumulation. This observation is reminiscent of Pbx/Meis relationships in bilaterians (<xref ref-type="bibr" rid="bib1">Abu-Shaar et al., 1999</xref>; <xref ref-type="bibr" rid="bib56">Saleh et al., 2000</xref>). We further confirmed this result by visualizing <italic>Nv</italic>Pbx/<italic>Nv</italic>Meis complexes directly in live <italic>Nematostella</italic> embryos through BiFC (Bimolecular Complementation Fluorescence). BiFC relies on the property of fluorescent proteins to be reconstituted when their two non-fluorescent sub-fragments are close enough in space. This method has been developed in several animal model systems to validate interactions between two candidate partners in vivo (<xref ref-type="bibr" rid="bib37">Kodama and Hu, 2012</xref>). In this study, we co-expressed <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis fused respectively to the N-terminal (VN) or C-terminal (VC) fragment of Venus. This resulted in fluorescent signals in the cytoplasm (where interaction occurs first) and nuclei of embryonic cells (<xref ref-type="fig" rid="fig3">Figure 3B</xref>). No BiFC was obtained between a fusion construct and the complementary isolated VC or VN fragment, highlighting that the interaction between <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis fusion proteins was not artificially induced by the inherent affinity of the VN and VC fragments (<xref ref-type="fig" rid="fig3">Figure 3B</xref>).<fig id="fig3" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.009</object-id><label>Figure 3.</label><caption><title>Hox and TALE members form protein complexes in vivo.</title><p>(<bold>A</bold>) <italic>Nv</italic>Pbx interacts with <italic>Nv</italic>Meis in vivo. The nuclear localisation of a fusion mCherry-<italic>Nv</italic>Pbx protein was only observed upon co-injection with <italic>Nv</italic>Meis. Graphs on the left are quantifications of the ratio between nuclear and cytoplasmic fluorescent signals (log2). Note that mCherry-<italic>Nv</italic>Pbx alone did not lead to any signal, suggesting that the fusion protein is not stable in the absence of Meis, as noticed in bilaterians. (<bold>B</bold>) BiFC between <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis in the Nematostella embryo. Fusion constructs are schematized on the left. VN: N-terminal fragment of Venus; VC: C-terminal fragment of Venus. Specificity of BiFC is verified by the absence of fluorescent signals upon the injection of isolated VN or VC fragments, together or with the complementary VC-<italic>Nv</italic>Meis or VN-<italic>Nv</italic>Pbx fusion proteins, as indicated. Interaction between <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis occurs both in the cytoplasm and nucleus (see text for details). (<bold>C</bold>) BiFC between <italic>Nv</italic>HoxE and <italic>Nv</italic>Pbx in the Nematostella embryo. Interaction occurs only in the nucleus. Mutation of the residue 54 in the homeodomain (HD) of <italic>Nv</italic>Pbx abolishes DNA-binding and BiFC with <italic>Nv</italic>HoxE. In all panels, Dapi (cyan) stains nuclei and Dextran (red) is a control of injection conditions.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.009">http://dx.doi.org/10.7554/eLife.01939.009</ext-link></p></caption><graphic xlink:href="elife01939f003"/></fig></p><p>BiFC was also used to visualize interactions between <italic>Nv</italic>Pbx and <italic>Nv</italic>HoxE (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). The specificity of this interaction was validated by the absence of BiFC between <italic>Nv</italic>HoxE and a DNA-binding deficient form of <italic>Nv</italic>Pbx (<xref ref-type="fig" rid="fig3">Figure 3C</xref>), showing that the formation of the cnidarian Hox/Pbx complex is DNA-binding dependent, as previously noticed in bilaterians (<xref ref-type="bibr" rid="bib28">Hudry et al., 2011</xref>, <xref ref-type="bibr" rid="bib29">2012</xref>). Altogether, these results show that <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis are co-expressed with several <italic>Nv</italic>Hox genes in the endoderm and that <italic>Nv</italic>Hox and <italic>Nv</italic>TALE proteins can constitute an interaction network in vivo.</p></sec><sec id="s2-2"><title>Interaction properties between <italic>Nematostella</italic> and bilaterian Hox/TALE complexes are highly similar in vitro</title><p>Next, we analysed the molecular properties underlying the assembly of <italic>Nematostella</italic> Hox/Pbx/Meis complexes in vitro. <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis proteins were previously shown to interact with bilaterian Hox proteins (<xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>). Here, we conducted binding assays with <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE proteins and assembly properties of protein complexes were measured by electromobility shift assays (EMSAs) on three different DNA probes. DNA probes differ by one nucleotide in the Hox/Pbx binding site (<xref ref-type="fig" rid="fig4">Figure 4A</xref>), each one corresponding to the preferential DNA-binding sites of previously defined anterior, central, and posterior Hox/Pbx complexes with vertebrate and invertebrate proteins (<xref ref-type="bibr" rid="bib59">Shen et al., 1996</xref>; <xref ref-type="bibr" rid="bib63">Slattery et al., 2011</xref>).<fig-group><fig id="fig4" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.010</object-id><label>Figure 4.</label><caption><title>Interaction properties between <italic>Nv</italic>Hox and <italic>Nv</italic>TALE proteins in vitro.</title><p>(<bold>A</bold>) Nucleotide sequence of the different classes of Hox/Pbx binding sites used in band shift experiments. The nucleotide that distinguishes each Hox/Pbx binding site is bolded. (<bold>B</bold>–<bold>B′</bold>) Band shift experiments between <italic>Nv</italic>HoxB or <italic>Nv</italic>HoxE and <italic>Nv</italic>Pbx on the three different classes of binding sites, as indicated. Coloured and grey arrows point to monomer or dimer binding, respectively. Graph on the right (<bold>B′</bold>) depicts the relative affinity of each dimeric complex on the three different binding sites, as deduced from the direct quantification on the gel (values are indicated at the bottom). (<bold>C</bold>) Band shift experiments between wild-type or HX-mutated <italic>Nv</italic>Hox proteins and <italic>Nv</italic>TALE cofactors, as indicated. Colour codes and annotations are as in (<bold>B</bold>). Black arrow indicates trimeric <italic>Nv</italic>Hox/<italic>Nv</italic>Pbx/<italic>Nv</italic>Meis complexes. Other bands are not specific (proteins of the lysate). Black scare highlights the supershift band resulting from the addition of an antibody against the HA tag of <italic>Nv</italic>Hox proteins. Asterisk shows the free probe. Note that the loss of dimeric <italic>Nv</italic>Hox/<italic>Nv</italic>Pbx complex upon the HX mutation is rescued in the presence of <italic>Nv</italic>Meis.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.010">http://dx.doi.org/10.7554/eLife.01939.010</ext-link></p></caption><graphic xlink:href="elife01939f004"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.011</object-id><label>Figure 4—figure supplement 1.</label><caption><title>Protein sequence alignment between <italic>Nv</italic>HoxE (upper sequence) and <italic>Nv</italic>HoxB (lower sequence).</title><p>The HX motif and HD are highlighted in red and yellow, respectively. A typical HX possesses a core tryptophan residue in a hydrophobic context, with a lysine or arginine residue at position +2 to +5 (<xref ref-type="bibr" rid="bib30">In der Rieden et al., 2004</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.011">http://dx.doi.org/10.7554/eLife.01939.011</ext-link></p></caption><graphic xlink:href="elife01939fs005"/></fig></fig-group></p><p>We observed that <italic>Nv</italic>HoxB/<italic>Nv</italic>Pbx and <italic>Nv</italic>HoxE/<italic>Nv</italic>Pbx complexes display anterior and central DNA-binding preferences, respectively (<xref ref-type="fig" rid="fig4">Figure 4B–B′</xref>). The addition of a consensus Meis binding site in a topology found in known Hox target enhancers (<xref ref-type="bibr" rid="bib41">Mann et al., 2009</xref>) confirmed that <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE do form trimeric complexes with the TALE partners on DNA (<xref ref-type="fig" rid="fig4">Figure 4C</xref>). Interestingly, the DNA-binding of <italic>Nv</italic>Meis is also sufficient for rescuing the loss of <italic>Nv</italic>Hox/<italic>Nv</italic>Pbx complex formation upon the HX mutation (<xref ref-type="fig" rid="fig4">Figure 4C</xref>), suggesting that <italic>Nv</italic>Meis is able to remodel <italic>Nv</italic>Hox–<italic>Nv</italic>Pbx interactions. Given the sequence divergence between the two <italic>Nv</italic>Hox proteins (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>), these alternative interaction modes are presumably paralog-specific, as previously suggested in bilaterians (<xref ref-type="bibr" rid="bib46">Merabet et al., 2007</xref>; <xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>).</p></sec><sec id="s2-3"><title>Genomic binding sites for <italic>Nv</italic>Hox and <italic>Nv</italic>TALE proteins are preferentially localized in the promoter region of genes expressed in the endoderm and allow the assembly of Hox/TALE complexes in vitro</title><p>Our band shift assays were performed on consensus binding sites previously defined with bilaterian Hox and TALE proteins. To know whether such sites could be used in the context of <italic>Nematostella</italic> development, we searched for their presence in the <italic>Nematostella</italic> genome. We predicted that these DNA-binding sites should be found in the promoter region of genes expressed in the endoderm, where Hox and TALE products are present together. By comparison, the promoter region of genes expressed in the ectoderm should not be enriched in Pbx/Meis-binding sites since the TALE partners are absent in this tissue. Therefore, we performed an in silico analysis based on 76 genes displaying a characterized developmental expression pattern during <italic>Nematostella</italic> embryogenesis. The choice of working with a limited number of genes was motivated by the fact that we did not find any significant enrichment of Hox/PBC/Meis binding sites in a genome-wide search, neither in <italic>Nematostella</italic> nor in other metazoan species (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>). In addition, by limiting the search in non-coding regions (of at least 60 base pairs) conserved in 12 <italic>Drosophila</italic> genomes, we could find a higher density of Hox/PBC/Meis clusters (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>). These results highlight that the signal to noise ratio is too low when considering Hox/PBC/Meis binding sites in all non-coding regions, and that the space search needs to be restricted to observe a significant enrichment.</p><p>Our in silico analysis revealed a significant enrichment of Hox/Pbx binding sites in the promoter region of genes expressed in the endoderm compared to the ectoderm (<xref ref-type="fig" rid="fig5">Figure 5A,B</xref>, ‘Materials and methods’). Several of these genes also contain a consensus Meis binding sequence within the 40 nucleotides surrounding the Hox/Pbx binding site (<xref ref-type="fig" rid="fig5">Figure 5C</xref>, ‘Materials and methods’). Among the candidate target genes containing a putative Hox/Pbx/Meis binding site in their promoter region, we found <italic>NvHoxB</italic> and <italic>NvHoxC</italic>. Thus, auto/cross-regulatory loops may occur between <italic>Nv</italic>Hox genes, as observed in bilaterians. Since sequences surrounding Hox/TALE binding sites can also strongly influence the protein complex formation (<xref ref-type="bibr" rid="bib16">Ebner et al., 2005</xref>; <xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>), we verified that the binding sites found in proximity of <italic>NvHoxB</italic> and <italic>NvHoxC</italic> could indeed allow the assembly of Hox/TALE complexes in vitro. We confirmed that <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE could form dimeric or trimeric complexes on these putative binding sites. Interestingly, <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE displayed distinct DNA-binding preferences on these two sites (<xref ref-type="fig" rid="fig5">Figure 5D–D′</xref>). Again, the assembly of <italic>Nematostella</italic> Hox/Pbx complexes was HX-dependent on both probes, except in the presence of <italic>Nv</italic>Meis, highlighting that alternative interaction modes between <italic>Nematostella</italic> Hox and TALE proteins can occur on various DNA-binding sites (<xref ref-type="fig" rid="fig5s2">Figure 5—figure supplement 2</xref>). Altogether these results show that the molecular properties underlying the Hox-TALE system are conserved between Cnidaria and Bilateria.<fig-group><fig id="fig5" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.012</object-id><label>Figure 5.</label><caption><title>Genes expressed in the endoderm are enriched in Hox-TALE binding sites in their promoter region.</title><p>(<bold>A</bold>) Hox/Pbx binding motifs represented as logos. The three motifs represent the binding specificity of the Hox/Pbx complex for sites of class I, II, or III. Matrix was determined by Selex with the Drosophila proteins (<xref ref-type="bibr" rid="bib63">Slattery et al., 2011</xref>). (<bold>B</bold>) Score distributions of the Hox/Pbx Class III matrix. The Y-axis is shown in logarithmic scale to highlight the relevant range of p values (small values). The separation of the pink curve (endoderm) from the black one (theoretical distribution) indicates an enrichment of the Hox/Pbx putative binding sites in the promoter of genes expressed in the endoderm. On the contrary, there is no enrichment in the promoter of genes expressed in the ectoderm, as the orange curve follows the black one. All negative controls also show no enrichment: random sets of gene promoters (cyan), promoter regions randomized by matrix column permutations for the endoderm (light pink) and ectoderm (light orange). (<bold>C</bold>) In silico analysis of Hox/Pbx/Meis binding sites in the promoter region (1 kb or 2 kbs upstream of the transcription start site) of genes expressed in the endoderm (pink), ectoderm (orange), or randomly chosen (cyan). The graph illustrates the preferential enrichment of Hox/Pbx/Meis binding sites in the promoter region of endodermal genes. Rm: repeat masked. (<bold>D</bold>–<bold>D′</bold>) Band shift experiments between <italic>Nv</italic>Hox and <italic>Nv</italic>TALE proteins on binding sites found in the promoter region of <italic>NvHoxB</italic> and <italic>NvHoxC</italic> genes. Sequence and genomic position of each binding site are shown above the gel. Colour code and annotations are as in <xref ref-type="fig" rid="fig3">Figure 3</xref>. Note the distinct DNA-binding preferences of <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE on these two different target sites. See also <xref ref-type="fig" rid="fig5s1 fig5s2">Figure 5—figure supplements 1 and 2</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.012">http://dx.doi.org/10.7554/eLife.01939.012</ext-link></p></caption><graphic xlink:href="elife01939f005"/></fig><fig id="fig5s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.013</object-id><label>Figure 5—figure supplement 1.</label><caption><title>Genome-wide analysis cannot reveal significant enrichment of Hox/PBC/Meis binding sites.</title><p>(<bold>A</bold>) Density of Hox/PBC/Meis clusters in the genome of various organisms. The density was calculated on all non-coding regions of the genomes (blue-filled bars), repeat-masked except for <italic>Amphimedon</italic> where the repeat-masked genome was the same as the non-repeat-masked one. Two other conditions (white bars) represent a subset of the genome. The non-coding regions (CNE) conserved in 12 Drosophila genomes show a higher density than genome-wide approaches. These results suggest that the search space needs to be reduced to obtain a good signal/noise ratio. One idea would be to search for conserved regions within cnidarians, taking Nematostella as reference, but such an analysis was beyond the scope of this project, and the divergence time of available cnidarian genomes might not be adapted to this analysis. We attempted a related analysis by taking microsyntenic regions as described in <xref ref-type="bibr" rid="bib31">Irimia et al. (2012)</xref>. The results do not show a high density comparable to the Drosophila CNEs. We hypothesize that these microsyntenic regions still have a low signal to noise ratio for these motif clusters, or that biologically, the Hox/Pbx + Meis cluster is not majorly involved in the regulation taking place at these regions conserved throughout metazoans. (<bold>B</bold>) Validation of cluster enrichment. For each organism, we calculated the enrichment of Hox/PBC/Meis clusters, compared to a random control. At first, we conducted this analysis on random sequences, artificially generated from Markov models trained on the genomes of interest, and taking into account the number and positions of the repeats. The results, however, were highly dependent on the order of the Markov model. To circumvent this, we used randomized motifs as a control, allowing us to keep working on the real genomic sequences. We permuted the motif positions 100 times, allowing, removing the biological signal, while retaining the statistical properties of the PSSMs describing the motifs. We observed a clear enrichment of the clusters in Drosophila CNEs. In contrast, most of the genome-wide analyses did not reveal any enrichment, except in Drosophila, which showed a slight enrichment similar to <italic>Trichoplax</italic>. As Trichoplax has no HX-containing ANTP proteins (therefore no Hox/PBC/Meis network), with signal to noise ratio still quite low, we did not consider this slight enrichment.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.013">http://dx.doi.org/10.7554/eLife.01939.013</ext-link></p></caption><graphic xlink:href="elife01939fs006"/></fig><fig id="fig5s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.014</object-id><label>Figure 5—figure supplement 2.</label><caption><title><italic>Nv</italic>Meis promotes HX-independent interaction modes on DNA-binding sites found in the promoter region of <italic>NvHoxB</italic> (A) and <italic>NvHoxC</italic> (B).</title><p>Band shift experiments are performed with wild-type or HX-mutated forms of <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE, in the presence of <italic>Nv</italic>TALE cofactors, as indicated. Loss of dimeric <italic>Nv</italic>Hox/<italic>Nv</italic>Pbx complexes upon the HX mutation is rescued in the presence of <italic>Nv</italic>Meis. Values of the interaction levels are shown at the bottom of the gel. Asterisk marks the free probe. Black arrowhead (left) corresponds to the dimeric <italic>Nv</italic>Pbx/<italic>Nv</italic>Meis complex. Coloured, grey, and black arrows (right) show monomer, dimer, and trimer DNA-binding complexes, respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.014">http://dx.doi.org/10.7554/eLife.01939.014</ext-link></p></caption><graphic xlink:href="elife01939fs007"/></fig></fig-group></p></sec><sec id="s2-4"><title><italic>Nematostella</italic> Hox and TALE proteins can execute generic functions in invertebrate and vertebrate species</title><p>To assess whether the <italic>Nematostella</italic> Hox/TALE system could have any conserved biological function, we examined the activity of <italic>Nv</italic>Hox and <italic>Nv</italic>TALE proteins in two different bilaterian organisms, the fly <italic>Drosophila melanogaster</italic> and the frog <italic>Xenopus laevis</italic>.</p><p>For Hox assays, series of EMSAs previously confirmed that <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE are able to associate with the <italic>Drosophila</italic> Pbx (Extradenticle, Exd) and Meis (Homothorax, Hth) cofactors on different <italic>Drosophila</italic> Hox target enhancers in vitro (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>). Of note, <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE again display anterior or central-like DNA-binding preferences on those physiological target sites, respectively. Furthermore, BiFC validated that <italic>Nv</italic>Hox proteins could interact with Exd in vivo (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>). Again, the specificity of BiFC was confirmed with a DNA-binding deficient form of Exd (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>).</p><p>The activity of <italic>Nv</italic>Hox proteins in <italic>Drosophila</italic> was then measured in two generic Hox assays: the antenna-to-leg transformation in adult (<xref ref-type="bibr" rid="bib8">Casares et al., 1996</xref>; <xref ref-type="bibr" rid="bib68">Yao et al., 1999</xref>), and the rescue of the Hox <italic>labial</italic> (<italic>lab</italic>) mutant phenotype in a particular structure of the central nervous system called the tritocerebrum (<xref ref-type="bibr" rid="bib27">Hirth et al., 1998</xref>). We found that <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE were able to successfully function as their <italic>Drosophila</italic> homologs in both assays (<xref ref-type="fig" rid="fig6">Figure 6A,B</xref>). The antenna-to-leg transformation by <italic>Nv</italic>Hox proteins was shown to rely on the assembly of a repressive trimeric complex with <italic>Drosophila</italic> TALE cofactors on cis-regulatory sequences of the <italic>spineless</italic> (<italic>ss</italic>) target gene (<xref ref-type="fig" rid="fig6">Figure 6A</xref>, <xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>; <xref ref-type="bibr" rid="bib15">Duncan et al., 2010</xref>). Moreover, <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE behave like central and anterior paralogs in the tritocerebrum, respectively (<xref ref-type="fig" rid="fig6">Figure 6B</xref>, <xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>; <xref ref-type="bibr" rid="bib27">Hirth et al., 1998</xref>). Finally, the activity of both <italic>Nv</italic>Hox proteins in the antenna and tritocerebrum appears to be dependent on the integrity of the HX motif (<xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>).<fig-group><fig id="fig6" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.015</object-id><label>Figure 6.</label><caption><title>Functional analysis of <italic>Nv</italic>Hox and <italic>Nv</italic>Pbx proteins in Drosophila.</title><p>(<bold>A</bold>) Antenna-to-leg transforming activities of <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE. <italic>Nv</italic>Hox proteins were expressed in the antenna with the <italic>Distalless (Dll)-Gal4</italic> driver. Asterisk depicts leg-specific bracted bristles. 4–5 shows the transformation of the arista in two tarsal segments. Arrow and arrowhead in the enlargement indicate the formation of the leg-specific terminal claw and its associated sensory pad respectively. The antenna-to-leg transformation by <italic>Nv</italic>Hox proteins (grey) is achieved through the repression of the <italic>spineless</italic> (<italic>ss</italic>) target gene, as observed by the repression of the <italic>ss</italic> enhancer <italic>D4</italic> activity on <italic>lacZ</italic> reporter gene expression (orange). See also <xref ref-type="fig" rid="fig6s1 fig6s2">Figure 6—figure supplements 1 and 2</xref>. (<bold>B</bold>) Rescue of the <italic>labial</italic> (<italic>lab</italic>) mutant phenotype in the tritocerebrum by <italic>Nv</italic>Hox proteins. The central nervous system is stained with an anti-HRP (orange). Hox or GFP (as a control) proteins (grey) are expressed in the tritocerebrum with a <italic>lab-Gal4</italic> driver. Frontal connectives (asterisk), longitudinal connectives (arrowhead) and tritocerebral commissure (arrow) are indicated. In <italic>lab</italic> mutant background, longitudinal connectives are reduced, frontal connectives project ectopically and the tritocerebral commissure is missing (<xref ref-type="bibr" rid="bib27">Hirth et al., 1998</xref>). Expression of <italic>NvHoxB</italic> or <italic>NvHoxE</italic> in this mutant context leads to a complete or strong rescue of this phenotype, respectively. See also <xref ref-type="fig" rid="fig6s2">Figure 6—figure supplement 2</xref>. (<bold>C</bold>–<bold>C′</bold>) <italic>Nv</italic>Pbx can rescue zygotic <italic>exd</italic> mutant phenotypes in the Drosophila larva cuticle. (<bold>C</bold>) Larvae homozygous for the zygotic <italic>exd</italic><sup><italic>XP11</italic></sup> mutation have T3 and A1 segments that resemble to a T1/abdominal or A3 segment, respectively. Thoracic expression of either <italic>Dm</italic>Exd or <italic>Nv</italic>Pbx in this mutant background (through the UAS/Gal4 system, with the <italic>Antennapedia (Antp)-Gal4</italic> driver) is sufficient to restore the correct specification of T3 and A1, as assessed by the shape and arrangement of denticle belts. (<bold>C′</bold>) Ubx normally specifies the A1 segment. Ectopic expression of Ubx with <italic>Antp-Gal4</italic> induces A1-like segments in the thorax. In absence of Exd, Ubx produces A2-like segments. Providing back <italic>Nv</italic>Pbx in this genetic background is sufficient to restore the normal A1-inducing activity of Ubx. See also <xref ref-type="fig" rid="fig6s3 fig6s4">Figure 6—figure supplements 3 and 4</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.015">http://dx.doi.org/10.7554/eLife.01939.015</ext-link></p></caption><graphic xlink:href="elife01939f006"/></fig><fig id="fig6s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.016</object-id><label>Figure 6—figure supplement 1.</label><caption><title><italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE interact with the Drosophila TALE cofactors Extradenticle (Exd) and Homothorax (Hth) in vitro and in vivo.</title><p>(<bold>A</bold> and <bold>B</bold>) Band shift experiments on physiological target sequences of Drosophila Hox proteins. Probes derived from the auto-regulatory element of the Hox genes <italic>labial</italic> (<italic>lab48/95</italic>, <bold>A</bold>) and <italic>Deformed</italic> (<italic>Dfd</italic>, <italic>modCsite 1</italic>, <bold>B</bold>), corresponding to binding sites of class I or II, respectively. Colour codes and annotations are as in <xref ref-type="fig" rid="fig5s2">Figure 5—figure supplement 2</xref>. Unfilled arrows indicate DNA-binding complexes with Drosophila Hox (<italic>Dm</italic>Lab and <italic>Dm</italic>Dfd) and TALE (<bold>E</bold> and <bold>H</bold>) proteins. Grey scare in (<bold>B</bold>) indicates the supershift band resulting from the addition of an antibody against the HA tag of <italic>Nv</italic>Hox proteins. (<bold>C</bold>) Visualisation of interactions between <italic>Nv</italic>Hox proteins and Exd by BiFC in a live stage 10 Drosophila embryo. Fusion constructs are schematized above each picture. Constructs were expressed with the <italic>engrailed (en)-Gal4</italic> driver. Specificity of BiFC was verified with the Exd fusion construct mutated in the residue 54 of the HD.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.016">http://dx.doi.org/10.7554/eLife.01939.016</ext-link></p></caption><graphic xlink:href="elife01939fs008"/></fig><fig id="fig6s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.017</object-id><label>Figure 6—figure supplement 2.</label><caption><title>Role of the HX of <italic>Nv</italic>Hox proteins in generic Drosophila Hox assays.</title><p>(<bold>A</bold>) Antenna-to-leg transforming activities of <italic>Nv</italic>Hox proteins do not rely on the repression of <italic>homothorax</italic> (<italic>hth</italic>) target gene. Expression of <italic>Nv</italic>HoxB (grey) in the proximal part of the antenna imaginal disc has no effect on <italic>hth</italic> expression (as assessed by an immunostaining against Hth, orange). By comparison, expressing the Drosophila Antennapedia (Antp) in the same condition leads to a complete loss of Hth. (<bold>B</bold>) The HX mutation abolishes complex formation between <italic>Nv</italic>HoxB and Drosophila TALE cofactors on the target binding sites of the <italic>spineless D4</italic> regulatory element. Colour codes and annotations are as in <xref ref-type="fig" rid="fig5s2">Figure 5—figure supplement 2</xref>. (<bold>C</bold>) The HX mutation affects the repressive activity of <italic>Nv</italic>HoxB on the <italic>spineless D4</italic> target element in vivo. Proteins were expressed as in (<bold>A</bold>). Expression of <italic>D4</italic> was indirectly quantified through immunostaining against the <italic>D4</italic>-driven LacZ reporter protein (orange). (<bold>D</bold>–<bold>E′</bold>) The HX mutation abolishes the rescue activity of Drosophila and Nematostella Hox proteins in the tritocerebrum of <italic>labial</italic> (<italic>lab</italic>) mutant embryos. (<bold>D</bold>–<bold>D′</bold>) Rescue assays with wild-type Hox proteins, as indicated. (<bold>E</bold>–<bold>E′</bold>) Rescue assays with HX-mutated Hox proteins, as indicated. The central nervous system is stained with an anti-HRP (orange). HA-tagged proteins (grey) were expressed in the tritocerebrum with a <italic>lab-Gal4</italic> driver. For quantifications of rescue efficiency (<bold>D′</bold>–<bold>E′</bold>), 100 embryos were examined in each case. Percentage values were corrected in order to take into account the phenotypic penetrance of the <italic>lab</italic> mutation in tritocerebral development (90%). The rescue efficiency of <italic>Dmlab</italic> was used as a standard and taken as 100%. The rescue values (the relative percentage of embryos showing a complete rescue of the tritocerebral brain defects) of <italic>Dm</italic>Hox and <italic>NvHox</italic> gene products are shown in percentage relative to <italic>Dmlab</italic>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.017">http://dx.doi.org/10.7554/eLife.01939.017</ext-link></p></caption><graphic xlink:href="elife01939fs009"/></fig><fig id="fig6s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.018</object-id><label>Figure 6—figure supplement 3.</label><caption><title><italic>Nv</italic>Pbx interacts with the Drosophila Ultrabithorax (Ubx) and Homothorax (Hth) proteins in vitro and in vivo.</title><p>(<bold>A</bold>) Band shift experiments on DNA-binding sites derived from the regulatory elements of the <italic>Distalless</italic> (<italic>DllR</italic>) and <italic>teashirt</italic> (<italic>tsh</italic>) Hox target genes. Colour code and annotations are as in previous figures. (<bold>B</bold>–<bold>C</bold>) <italic>Nv</italic>Pbx interacts with Ubx (<bold>B</bold>) and Hth (<bold>C</bold>) in vivo. Fusion proteins generated for BiFC are schematized above the pictures. Expression was conducted with the <italic>Ubx-Gal4</italic> driver. Pictures were acquired in a live stage 10 embryo.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.018">http://dx.doi.org/10.7554/eLife.01939.018</ext-link></p></caption><graphic xlink:href="elife01939fs010"/></fig><fig id="fig6s4" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.019</object-id><label>Figure 6—figure supplement 4.</label><caption><title><italic>Nv</italic>Meis reproduces generic bilaterian Meis activities in the Xenopus embryo.</title><p>While more anterior hindbrain marker genes are not expressed (<italic>krox20</italic>, <italic>hoxd1</italic> and <italic>hoxd3</italic>), more posterior spinal cord marker genes such as, <italic>hoxa7</italic>, <italic>hoxb7</italic>, <italic>hoxb9</italic>, <italic>hoxc10</italic>, <italic>hoxd10</italic>, <italic>cdx1</italic>, <italic>cdx2</italic> and <italic>cdx4</italic> are robustly induced upon injection of <italic>Nv</italic>Meis in the embryo. Total RNA was isolated from five control embryos (CE) and eighteen animal caps (AC) from the control or injected groups. Semi-quantitative RT-PCR analysis was performed on AC explants that were removed from control (non injected, RT) and injected embryos cultured until the neurula stage 16. <italic>EF1α</italic>controls for RNA levels in each sample. A comparative level of genes induction by <italic>X</italic>Meis3 is provided on the right.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.019">http://dx.doi.org/10.7554/eLife.01939.019</ext-link></p></caption><graphic xlink:href="elife01939fs011"/></fig></fig-group></p><p>The functional conservation of <italic>Nv</italic>Pbx was addressed by analysing its potential to rescue zygotic <italic>exd</italic> mutant phenotypes in <italic>Drosophila</italic>. As for <italic>Nv</italic>Hox proteins, we previously verified that <italic>Nv</italic>Pbx is able to form a protein complex with <italic>Drosophila</italic> Hox and Meis proteins in vitro and in vivo (<xref ref-type="fig" rid="fig6s3">Figure 6—figure supplement 3</xref>). We observed that <italic>Nv</italic>Pbx could rescue the <italic>exd</italic> mutant phenotype in the <italic>Drosophila</italic> larva cuticle (<xref ref-type="fig" rid="fig6">Figure 6C</xref>). Providing <italic>Nv</italic>Pbx in this mutant background was also sufficient to rescue the A1 transforming activity of Ubx (<xref ref-type="fig" rid="fig6">Figure 6C′</xref>), which is also known to depend on the integrity of the HX (<xref ref-type="bibr" rid="bib20">Galant et al., 2002</xref>). These results highlight that <italic>Dm</italic>Exd and <italic>Nv</italic>Pbx are functionally equivalent, at least for specification functions in the <italic>Drosophila</italic> epidermis.</p><p>Finally, the functional conservation of <italic>Nv</italic>Meis was measured in the <italic>Xenopus</italic> embryo, which constitutes a well-established developmental model system for assessing Meis activities. In particular, <italic>X</italic>Meis proteins are known to be required for the specification of posterior cell fates along the AP axis of the central nervous system (<xref ref-type="bibr" rid="bib13">Dibner et al., 2001</xref>), a function that also involves Pbx1 (<xref ref-type="bibr" rid="bib40">Maeda et al., 2001</xref>). Accordingly, ectopic expression of <italic>X</italic>Meis proteins causes anterior neural truncations with a concomitant expansion of hindbrain and spinal cord (<xref ref-type="bibr" rid="bib57">Salzberg et al., 1999</xref>). This phenotype is reproduced with the fly or mouse Meis proteins, demonstrating that it can constitute a generic assay for assessing Meis function. We observed that the injection of <italic>Nv</italic>Meis in animal caps of <italic>Xenopus</italic> embryos was also able to robustly induce the expression of several posterior spinal cord marker genes (like <italic>Hoxa7</italic>, <italic>cdx1</italic> or <italic>cdx2</italic>), although to a lesser extent than <italic>X</italic>Meis3 (<xref ref-type="fig" rid="fig6s4">Figure 6—figure supplement 4</xref>). Thus, <italic>Nv</italic>Meis displays a striking functional similarity with its bilaterian homologs.</p><p>In sum, our assays highlight a striking functional conservation between <italic>Nematostella</italic> and bilaterian Hox and TALE proteins, suggesting that the Hox/TALE network was already at work in the common ancestor of Cnidaria and Bilateria.</p></sec><sec id="s2-5"><title>Genesis of Hox–TALE interaction networks across Metazoa</title><p>Among the ANTP class, we can distinguish three main subclasses that originally derived from a ProtoANTP ancestor (<xref ref-type="bibr" rid="bib55">Saina et al., 2009</xref>): Hox/ParaHox, NK and extended-Hox (<xref ref-type="fig" rid="fig7">Figure 7</xref>). Consistent with their close evolutionary relationships, Hox, NK and extended-Hox members share common protein features including the presence of an HX motif upstream of the HD (<xref ref-type="fig" rid="fig7">Figure 7</xref>). These observations raise the question of the molecular mechanisms that led to the emergence of the Hox-TALE network and more generally to interaction networks between TALE proteins and other members of the ANTP class across metazoan evolution. We postulated that the HX motif could have constituted a major protein scaffold that provided an ancestrally conserved TALE interaction potential to different ANTP members.<fig id="fig7" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.020</object-id><label>Figure 7.</label><caption><title>Phylogeny of Hox, Extended-Hox (Engrailed, En) and NK (Msx) proteins during eukaryote evolution.</title><p>Nomenclature is as in <xref ref-type="fig" rid="fig1">Figure 1</xref>. The conserved features of any HX motif correspond to a sequence containing an invariant tryptophan residue in a hydrophobic context, with a lysine or arginine residue at position +2 to +5, as previously defined (<xref ref-type="bibr" rid="bib30">In der Rieden et al., 2004</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.020">http://dx.doi.org/10.7554/eLife.01939.020</ext-link></p></caption><graphic xlink:href="elife01939f007"/></fig></p><p>To test this hypothesis, we started by analysing the interaction properties between NK and TALE proteins. Previous works showed that some vertebrate NK members could interact with PBC (<xref ref-type="bibr" rid="bib4">Brendolan et al., 2005</xref>) or PBC/Meis (<xref ref-type="bibr" rid="bib49">Rhee et al., 2004</xref>), but the role of the HX was not addressed in these interactions. Here, we analysed the molecular properties underlying complex assembly between the <italic>Nematostella</italic> NK representative <italic>Nv</italic>Msx and the two <italic>Nv</italic>TALE partners. We observed that <italic>Nv</italic>Msx is not able to interact with <italic>Nv</italic>Pbx except in the presence of <italic>Nv</italic>Meis (<xref ref-type="fig" rid="fig8">Figure 8A</xref>). Trimeric complex formation is however not as strong as with <italic>Nv</italic>Hox proteins and is also fully dependent on the integrity of the HX motif (<xref ref-type="fig" rid="fig8">Figure 8A</xref>).<fig-group><fig id="fig8" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.021</object-id><label>Figure 8.</label><caption><title>Genesis of Hox–TALE interaction networks in Metazoa.</title><p>(<bold>A</bold>) Band shift experiments between <italic>Nv</italic>Msx and <italic>Nv</italic>TALE cofactors, as indicated. Colour code and annotations are as in previous figures. Note that no dimeric <italic>Nv</italic>Msx/<italic>Nv</italic>Pbx complex is formed. Binding reactions with <italic>Nv</italic>Msx proteins were performed on a consensus <italic>Msx/Pbx</italic> binding site derived from vertebrates and containing an additional <italic>Meis</italic> binding site in a topology similar to the Hox probe (‘Materials and methods’). (<bold>B</bold>) Band shift experiments between wild-type, truncated or chimeric <italic>Nv</italic>Msx and/or <italic>Nv</italic>HoxB proteins, and <italic>Nv</italic>Pbx, as indicated. (<bold>C</bold>) Scheme of the diverse protein constructs and their corresponding interaction affinity level with <italic>Nv</italic>Pbx, as assessed from quantification of each band shift. Quantifications with truncated <italic>Nv</italic>Msx proteins were deduced by comparison with the trimeric <italic>Nv</italic>Msx/<italic>Nv</italic>Pbx/<italic>Nv</italic>Meis in (<bold>A</bold>). (<bold>D</bold>) Molecular rules underlying interaction properties between NK, Hox, or extended-Hox members and TALE cofactors in Eumetazoans. In this model, Meis is able to promote HX-dependent interactions between <italic>Nv</italic>Msx and <italic>Nv</italic>Pbx by masking inhibitory interaction domains in <italic>Nv</italic>Msx. Whether a similar role could exist in Bilateria remains to be determined. We noticed that the Drosophila Msx protein contains an HX and forms trimeric but not dimeric complexes with the Drosophila TALE partners (not shown). HX-dependency in those interactions remains to be determined (question marks). Interaction between <italic>Dm</italic>En and PBC is also HX-dependent but does not require the presence of Meis to occur. In contrast to the NK or extended-Hox families, most members of the Hox family have retained a HX motif. This motif is required for generic Hox/Pbx functions. The additional presence of Meis allows revealing specific Pbx interaction motifs (SPIMs), which could be important for distinguishing and/or diversifying the embryonic activities of each Hox paralog group member. See also <xref ref-type="fig" rid="fig8s1">Figure 8—figure supplement 1</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.021">http://dx.doi.org/10.7554/eLife.01939.021</ext-link></p></caption><graphic xlink:href="elife01939f008"/></fig><fig id="fig8s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.022</object-id><label>Figure 8—figure supplement 1.</label><caption><title>The Drosophila Engrailed (<italic>Dm</italic>En) protein forms HX-dependent DNA-binding complexes with Exd (<italic>Dm</italic>E) and Hth (H) on physiological target sites.</title><p>Colour code is as in previous figures. Monomer binding of <italic>Dm</italic>En is indicated by a green arrow.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.022">http://dx.doi.org/10.7554/eLife.01939.022</ext-link></p></caption><graphic xlink:href="elife01939fs012"/></fig></fig-group></p><p>Our results suggest that protein region(s) in <italic>Nv</italic>Msx could mask the interaction with Pbx in absence of Meis. We confirmed this hypothesis by testing a series of truncated and chimeric proteins generated from <italic>Nv</italic>Msx and <italic>Nv</italic>HoxB. We found that deleting the N- and C-terminal parts of <italic>Nv</italic>Msx allowed dimeric complex formation with <italic>Nv</italic>Pbx (<xref ref-type="fig" rid="fig8">Figure 8B,C</xref>). Conversely, the N- and C-terminal regions of <italic>Nv</italic>Msx are sufficient to alleviate the interaction between a minimal <italic>Nv</italic>HoxB protein and <italic>Nv</italic>Pbx (<xref ref-type="fig" rid="fig8">Figure 8B,C</xref>).</p><p>Together these results show that the NK-TALE and Hox-TALE interaction networks rely on different molecular properties, in particular with a role of Meis in promoting HX-dependent or HX-independent interaction modes, respectively (<xref ref-type="fig" rid="fig8">Figure 8D</xref>).</p><p>We next analysed the interaction properties between TALE proteins and the <italic>Drosophila</italic> Engrailed (En) protein, a member of the extended-Hox family, which was recently described to form cooperative DNA-binding complexes with Exd and Hth on physiological target sequences (<xref ref-type="bibr" rid="bib19">Fujioka et al., 2012</xref>). We observed that En could form dimeric or trimeric complexes with Exd or Exd/Hth respectively, but in all cases these complexes were lost upon the mutation of the HX (<xref ref-type="fig" rid="fig8s1">Figure 8—figure supplement 1</xref>).</p><p>In conclusion, although <italic>Nv</italic>Msx and <italic>Dm</italic>En do not exhibit identical cooperative DNA-binding properties with PBC and Meis, they both require the HX to interact with the TALE partners (<xref ref-type="fig" rid="fig8">Figure 8D</xref>). Thus, the acquisition of the HX motif during evolution was likely a key molecular event for the emergence of ANTP–TALE interaction networks. Along the same line, we observed that the Trox2/Gsx protein from <italic>Trichoplax adhaerens</italic>, which does not contain any obvious HX-like sequence (<xref ref-type="bibr" rid="bib58">Schierwater and Kuhn, 1998</xref>), is not able to form any dimeric or trimeric complex with PBC or PBC/Meis, respectively (<xref ref-type="fig" rid="fig9">Figure 9A</xref>).<fig-group><fig id="fig9" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.023</object-id><label>Figure 9.</label><caption><title>Interaction properties of Hox and TALE proteins from <italic>Trichoplax adhaerens</italic> and <italic>Acanthamoeba castellanii</italic>.</title><p>(<bold>A</bold>) The ProtoHox/ParaHox Trox2 protein from <italic>Trichoplax adhaerens</italic> does not form DNA-binding complexes with PBC or PBC/Meis in vitro. Band shift experiments are performed with mouse Pbx (<italic>Mm</italic>P) and Meis (<italic>Mm</italic>M) proteins on central (<italic>Meis-II</italic>) and posterior (<italic>Meis-III</italic>) Hox/PBC/Meis binding sites as indicated. Black arrowhead shows dimeric Pbx/Meis complexes. (<bold>B</bold>–<bold>D′</bold>) PBC (<italic>Ac</italic>P) and Meis (<italic>Ac</italic>M) proteins from the unicellular <italic>Acanthamoeba castellanii</italic> organism cannot form protein complexes between each other or with Hox proteins. (<bold>B</bold>) Band shift experiment on a consensus PBC binding site (<italic>PRS</italic>, <xref ref-type="bibr" rid="bib9">Chang et al., 1995</xref>). <italic>Ac</italic>P does not bind DNA, neither as a monomer nor with <italic>Ac</italic>M. A weak monomer DNA-binding of <italic>Ac</italic>M is observed (white arrowhead). This monomer binding is strongly enhanced in the presence of mouse Pbx1 (<italic>Mm</italic>P, black arrowhead). In comparison, <italic>Mm</italic>P binds strongly (grey arrow), and the monomer binding of Meis1 (<italic>Mm</italic>M) is also strongly enhanced in the presence of Pbx1 (black arrow). (<bold>C</bold>–<bold>C′</bold>) Band shift experiments with mouse HoxB8 (<italic>Mm</italic>HoxB8) and mouse or <italic>Acanthamoeba</italic> TALE cofactors on the central (<italic>Meis-II</italic>) Hox consensus binding probe as indicated. (<bold>D</bold>–<bold>D′</bold>) Band shift experiments with mouse HoxA9 (<italic>Mm</italic>HoxA9) and mouse or <italic>Acanthamoeba</italic> TALE cofactors on the posterior (<italic>Meis-III</italic>) Hox consensus binding probe as indicated. Complexes with Hox proteins are observed only with mouse Pbx (grey arrows) and Pbx/Meis partners (black arrows) on both probes. <italic>Ac</italic>Pbx and <italic>Ac</italic>Meis proteins are not able to form dimeric complexes on these probes, unlike mouse TALE proteins (black arrowheads). See also <xref ref-type="fig" rid="fig9s1">Figure 9—figure supplement 1</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.023">http://dx.doi.org/10.7554/eLife.01939.023</ext-link></p></caption><graphic xlink:href="elife01939f009"/></fig><fig id="fig9s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.024</object-id><label>Figure 9—figure supplement 1.</label><caption><title>PBC and Meis proteins from the unicellular <italic>Acanthamoeba castellanii</italic> organism do not form protein complexes with mouse HX-mutated Hox proteins.</title><p>(<bold>A</bold>) Band shift experiment with HX-mutated HoxB8 on a central consensus binding site (<italic>Meis II</italic>). (<bold>B</bold>) Band shift experiment with HX-mutated HoxA9 on a posterior consensus binding site (<italic>Meis III</italic>). Colour code and annotations are as in previous figures. Protein complexes are only observed with mouse proteins, as previously described (<xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.024">http://dx.doi.org/10.7554/eLife.01939.024</ext-link></p></caption><graphic xlink:href="elife01939fs013"/></fig></fig-group></p><p>To further confirm that ANTP-TALE networks are a metazoan innovation, we analysed the interaction properties of PBC and Meis proteins of <italic>Acanthamoeba castellanii (Ac</italic>), a unicellular organism from the Amoebozoa group (<xref ref-type="fig" rid="fig1">Figure 1</xref>). Interestingly, <italic>Ac</italic>Meis possesses a MEIS-A domain and displays a high level of sequence similarity with mouse or fly Meis proteins in the HD (<xref ref-type="fig" rid="fig2s2">Figure 2—figure supplement 2</xref>). In contrast, <italic>Ac</italic>Pbx lacks any PBC-A domain and has a strongly divergent HD when compared to other Pbx proteins (<xref ref-type="fig" rid="fig2s1">Figure 2—figure supplement 1</xref>). As expected, we observed that <italic>Ac</italic>Pbx could neither bind on a consensus PBC-binding site, nor stimulates the binding of <italic>Ac</italic>Meis on the same probe, suggesting that both proteins could not interact in vitro (<xref ref-type="fig" rid="fig9">Figure 9B</xref>). This result was confirmed by using central or posterior Hox/PBC/Meis binding sites, on which no dimeric or trimeric complex with Hox proteins could be formed (<xref ref-type="fig" rid="fig9">Figure 9C,D</xref>). To assess whether absence of protein complexes could be explained by the strong sequence divergence of <italic>Ac</italic>Pbx, we repeated experiments with the mouse Pbx1 protein. Under these heterologous partnership conditions, we observed that the binding of <italic>Ac</italic>Meis could be strongly enhanced in the presence of the Pbx partner, suggesting that the two proteins could make interactions (<xref ref-type="fig" rid="fig9">Figure 9B</xref>). However, neither dimeric nor trimeric complexes could be formed on central and posterior Hox/PBC/Meis nucleotide probes, demonstrating that <italic>Ac</italic>Meis lacks protein feature(s) for making cooperative DNA-binding complexes with Hox and PBC proteins (<xref ref-type="fig" rid="fig9">Figure 9C′–D′’</xref>). Not surprisingly, <italic>Ac</italic>Meis is also not able to rescue Hox/PBC complex formation upon the HX mutation (<xref ref-type="fig" rid="fig9s1">Figure 9—figure supplement 1</xref>).</p><p>Taken together, our results show that the use of other protein motifs than the HX for interaction with TALE partners is a peculiar property of Hox proteins among the ANTP class. They also emphasize that the PBC/Meis partnership likely evolved concomitantly with the apparition of the HX in the ANTP class. In this context, our work with TALE proteins of <italic>Acanthamoeba</italic> underlines that the evolution of the TALE partners enabled the interaction network with Hox proteins and hence new functions to emerge during eukaryote evolution.</p></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><sec id="s3-1"><title>Molecular evolution of the HX motif</title><p>We have shown that identical molecular rules and conserved functions characterize Hox-TALE interaction networks in Cnidaria and Bilateria. The presence of the HX motif in several <italic>Nv</italic>Hox members and its requirement for generic Hox/TALE functions strongly suggest that this motif had a pivotal role for the evolution of an active Hox-TALE system in early metazoan lineages. In addition, the observation that a number of cnidarian Hox proteins do not have any HX (<xref ref-type="fig" rid="fig10">Figure 10</xref>, <xref ref-type="fig" rid="fig10s1">Figure 10—figure supplement 1</xref>) highlights that the ancestral molecular properties and hence functions of the Hox-TALE network could have considerably diverged among different cnidarian lineages.<fig-group><fig id="fig10" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.025</object-id><label>Figure 10.</label><caption><title>Phylogeny of the HX in Hox proteins of main cnidarian lineages.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.025">http://dx.doi.org/10.7554/eLife.01939.025</ext-link></p></caption><graphic xlink:href="elife01939f010"/></fig><fig id="fig10s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.01939.026</object-id><label>Figure 10—figure supplement 1.</label><caption><title>Protein sequence alignment of the region encompassing the HX (highlighted in red) and HD (highlighted in yellow) of cnidarian Hox members used in <xref ref-type="fig" rid="fig10s1">Figure 10—figure supplement 1</xref>.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.026">http://dx.doi.org/10.7554/eLife.01939.026</ext-link></p></caption><graphic xlink:href="elife01939fs014"/></fig></fig-group></p><p>To date, no HX motif can be found in any member of the ANTP class in Porifera, Ctenophora, or Placozoa group. This motif is present in different ANTP subclasses, including NK, Hox/ParaHox and extended-Hox, specifically in Bilateria and Cnidaria. Different scenarios can be proposed for explaining the evolutionary history of the HX among different ANTP members. These scenarios are hypothetical and diverge according to the putative evolutionary history of the ANTP class homeobox genes. In one scenario, HX-containing NK, Hox and extended-Hox members could have emerged from a common HX-containing NK protein, which itself appeared from duplications of an ancestral HX-deficient NK cluster, at the basis of Eumetazoa (Bilateria+Cnidaria, <xref ref-type="fig" rid="fig11">Figure 11A</xref>). Alternatively, it was recently proposed that Hox/ParaHox, NK and extended-Hox evolved before the origin of poriferans (<xref ref-type="bibr" rid="bib45">Mendivil Ramos et al., 2012</xref>), being already present in the last common ancestor of animals (Urmetazoa). In this scenario, we do not favour the hypothesis of independent acquisitions of the HX in the three homeobox gene families. Indeed, although the HX is a short motif, it is always located upstream and at a reasonable distance of the HD. This invariant position is probably critical to ensure interactions with PBC proteins. Moreover, the distance between the HX and the HD could have played important roles for the acquisition of new functions, as noticed in certain bilaterian Hox proteins (<xref ref-type="bibr" rid="bib48">Prince et al., 2008</xref>; <xref ref-type="bibr" rid="bib54">Saadaoui et al., 2011</xref>). Thus, the HX could already have been present in the ProtoANTP protein of the Urmetazoa ancestor, being secondarily lost in Porifera, Ctenophora and Placozoa during evolution (<xref ref-type="fig" rid="fig11">Figure 11B</xref>).<fig id="fig11" position="float"><object-id pub-id-type="doi">10.7554/eLife.01939.027</object-id><label>Figure 11.</label><caption><title>Evolution of molecular signatures underlying interaction networks with TALE proteins.</title><p>(<bold>A</bold>) Model for the apparition of the HX in ANTP members of Cnidaria and Bilateria. In this scenario, the HX appeared in a duplicated NK protein that gave rise to other HX-containing ANTP members in the common ancestor of Bilateria and Cnidaria. Duplications in other lineages occurred without the apparition of the HX. (<bold>B</bold>) Second model for the apparition of the HX in ANTP members of Cnidaria and Bilateria. This model is based on a recent work postulating the existence of Hox/ParaHox, NK, and extended-Hox clusters in the common ancestor of animals (<xref ref-type="bibr" rid="bib45">Mendivil Ramos et al., 2012</xref>). In this scenario, it is unlikely that the HX appeared after duplications of the ProtoANTP ancestor independently and at the same place in the ProtoHox, ProtoNK and ProtoExtended(e)Hox families. Thus, the HX motif was probably already present in the ProtoANTP ancestor. This motif was secondarily lost in ANTP members of Porifera, Placozoa and Ctenophora during evolution. See also ‘Discussion’. (<bold>C</bold>) TALE proteins and the generation of interaction networks across major multicellular branches of the eukaryote evolutionary tree. TALE proteins are indicated in grey-filled boxes, with different grey tones corresponding to different TALE members. Other colours depict non-TALE members. Interactions can occur between different TALE members, or between TALE and non-TALE members. These interactions involve different proteins in each major multicellular branch, as indicated. Red signs in Metazoa symbolise interaction modes involving the HX or specific PBC interaction motifs (SPIMs) between TALE (PBC/Meis) and ANTP (NK, extended(e)Hox, Hox) members.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.01939.027">http://dx.doi.org/10.7554/eLife.01939.027</ext-link></p></caption><graphic xlink:href="elife01939f011"/></fig></p></sec><sec id="s3-2"><title>Hox/TALE functions in the sea anemone <italic>Nematostella vectensis</italic></title><p>Our results showed that <italic>Nematostella</italic> Hox and TALE proteins shared conserved functions with their bilaterian counterparts. Interestingly, <italic>Nv</italic>HoxB and <italic>Nv</italic>HoxE display anterior-like or central-like properties, respectively. These preferential activities were observed in vitro, at the level of DNA-binding site recognition, but also in the generic rescue assay of the <italic>Drosophila Hox</italic>-mutant tritocerebrum structure. Thus, although <italic>NvHoxB</italic> and <italic>NvHoxE</italic> are not organized in a genomic cluster, they display differential expression profiles and activities, suggesting that ancestral colinearity rules are at least kept for two asymmetrically expressed Hox genes in <italic>Nematostella</italic>.</p><p>Considering our in silico data, and given the expression profile of Hox and TALE members in the <italic>Nematostella</italic> embryo, we propose that Hox–TALE interaction networks could be used for regulating gene expression in the endoderm, likely for positioning and specifying the formation of the different mesenteries along the directive axis. Homology between cnidarian and bilaterian axes is a long-standing and still controversial question. It was first proposed that the oral–aboral axis of <italic>Nematostella</italic> could be orthologous to the bilaterian AP axis, with an anterior-like (<italic>NvHoxA</italic>/<italic>anthox6</italic>) and central/posterior (<italic>NvHoxF</italic>/<italic>Anthox1</italic>) Hox gene being expressed at the oral or aboral tip respectively (<xref ref-type="bibr" rid="bib18">Finnerty et al., 2004</xref>). This expression profile is however not conserved in other cnidarian species (<xref ref-type="bibr" rid="bib34">Kamm et al., 2006</xref>) and there is compelling evidence that the aboral pole could rather correspond to the anterior end of bilaterians (<xref ref-type="bibr" rid="bib61">Sinigaglia et al., 2013</xref>). Therefore, expression of <italic>Nv</italic>Hox genes along the primary body axis could correspond to individual morphogenetic and not positional patterning functions, as recently shown for <italic>NvHoxF</italic> (<xref ref-type="bibr" rid="bib61">Sinigaglia et al., 2013</xref>). In this context, other HD-containing determinants could play important patterning roles (<xref ref-type="bibr" rid="bib11">de Jong et al., 2006</xref>), as demonstrated for Six transcription factors in the early specification of the aboral pole (<xref ref-type="bibr" rid="bib61">Sinigaglia et al., 2013</xref>).</p><p>Along the same line, the directive axis of <italic>Nematostella</italic> was proposed to be homologous to the bilaterian DV axis (<xref ref-type="bibr" rid="bib43">Matus et al., 2006</xref>), but functional analyses revealed that DV patterning genes are also required in the endoderm and ectoderm along the primary axis (<xref ref-type="bibr" rid="bib43">Matus et al., 2006</xref>; <xref ref-type="bibr" rid="bib55">Saina et al., 2009</xref>).</p><p>Together, these observations highlight that patterning molecules can be used along different longitudinal axes during animal evolution, which renders difficult the comparison between Bilateria and Cnidaria. Here, we propose that the ancestral molecular cues underlying the Hox patterning system along the cnidarian directive axis could have been recruited for AP patterning in Bilateria.</p></sec><sec id="s3-3"><title>TALE proteins and the evolution of interaction networks in eukaryotes</title><p>Non-TALE and TALE representatives of the HD superfamily were probably already present in first eucaryotes (<xref ref-type="bibr" rid="bib12">Derelle et al., 2007</xref>; <xref ref-type="bibr" rid="bib38">Larroux et al., 2008</xref>; <xref ref-type="bibr" rid="bib52">Ryan et al., 2010</xref>), and it was proposed that interactions between these two classes of TFs could have existed in the common ancestor of plants, fungi, and metazoans (<xref ref-type="bibr" rid="bib6">Burglin, 1998</xref>). TALE proteins originate from a putative ancestor that contained a MEINOX domain and gave rise to conserved N-terminal interaction domains in different TALE members (<xref ref-type="bibr" rid="bib5">Burglin, 1997</xref>). Interestingly, although PBC and Meis are not present outside Unikonta, other TALE members are known to interact with each other or with other protein families in plants (<xref ref-type="bibr" rid="bib2">Bellaoui et al., 2001</xref>; <xref ref-type="bibr" rid="bib24">Hackbusch et al., 2005</xref>; <xref ref-type="bibr" rid="bib35">Kanrar et al., 2006</xref>; <xref ref-type="bibr" rid="bib25">Hay and Tsiantis, 2010</xref>) and fungi (<xref ref-type="bibr" rid="bib36">Keleher et al., 1989</xref>; <xref ref-type="bibr" rid="bib64">Stark and Johnson, 1994</xref>; <xref ref-type="bibr" rid="bib39">Li et al., 1998</xref>; <xref ref-type="bibr" rid="bib7">Carr et al., 2004</xref>), suggesting that partnership with TALE proteins is a common and ancient feature in eukaryotes (<xref ref-type="fig" rid="fig11">Figure 11C</xref>; <xref ref-type="bibr" rid="bib6">Burglin, 1998</xref>).</p><p>Here, we revealed the existence of interactions between typical HD (ANTP) and TALE (PBC/Meis) members in Cnidaria, suggesting that this network, which is also present in Bilateria, was already at work in the Eumetazoa ancestor, before the Cnidaria/Bilateria split. We showed that more ancient TALE proteins, like those from the unicellular <italic>Acanthamoeba</italic> organism could neither interact between each other nor form complexes with Hox proteins. Heterologous interaction assays between <italic>Ac</italic>Meis and mouse Hox and PBC proteins further exemplified that the PBC/Meis partnership is critical for the formation of Hox–TALE networks. This partnership probably appeared with the PBC-A domain in PBC, and concomitantly with the HX motif during eukaryote evolution. Although the MEIS-A domain was more ancient, the Meis partner also clearly acquired additional protein features, allowing the formation and therefore diversifying the activity of Hox/PBC/Meis networks in Metazoa.</p><p>Interestingly, the HX is not only conserved in the Hox family but also in different NK and extended-Hox members. Still, the role and the importance of TALE partners in these additional networks might not be equivalent. We propose that apparition of Hox, NK and extended-Hox members was accompanied by functional sub-specialisations that could in part result from divergent molecular interaction properties with TALE cofactors. For example, only two NK sub-family members (Msx and Tlx) have retained a HX motif, suggesting that interaction between NK and TALE proteins is not a general rule. The same rationale applies to extended-Hox members. On the contrary, the HX is present in almost all Hox paralog groups, which coincides with a general requirement of TALE cofactors in Hox functions. In this context, the role of Meis for revealing additional and more specific Pbx interaction motifs (SPIMs) in Hox proteins (<xref ref-type="bibr" rid="bib29">Hudry et al., 2012</xref>) was also likely an ancestral feature of the Hox/TALE system for distinguishing functions between different Hox paralog members.</p><p>In conclusion, we propose that Hox-TALE networks constituted an ancestral regulatory module that was later on exploited for patterning functions in Bilateria. This network was effective as soon as different interaction modes could exist with duplicated Hox family members, allowing diversifying patterning functions along the body axis. This original molecular system was subsequently co-opted by the various contexts of embryogenesis in different eumetazoan phyla, for axis or tissue (see e.g., <xref ref-type="bibr" rid="bib14">Di-Poi et al., 2007</xref>) patterning, illustrating its remarkable adaptability throughout animal evolution.</p></sec></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><sec id="s4-1"><title>Cloning</title><p>Clones were generated by PCR from full-length complementary DNAs and restriction-cloned in the appropriate vector (see also <xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref> for a complete list of all the constructs). Primers used are listed in <xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>. All constructs were sequence-verified before using.</p></sec><sec id="s4-2"><title>Fly stocks and transgenic lines</title><p>Transgenic lines were established either by the PhiC-31 integrase system (with the pUASTattB vector [<xref ref-type="bibr" rid="bib66">Venken et al., 2006</xref>; <xref ref-type="bibr" rid="bib3">Bischof et al., 2007</xref>]) or by classical P-element (with PUAST vector) mediated germ line transformation. Unless otherwise indicated, fly stocks were obtained from the Bloomington <italic>Drosophila</italic> Stock Center. Gal4 drivers used are: <italic>en</italic>-Gal4, <italic>Dll</italic>-Gal4, <italic>Ubx</italic>-Gal4<sup>M1</sup> (kindly provided by Ernesto Sanchez-Herrero), <italic>Antp</italic>-Gal4 (Michel Crozatier), and <italic>dpp</italic><sup><italic>blink</italic></sup>-Gal4. <italic>lab</italic><sup><italic>VD1</italic></sup>; <italic>lab</italic>-Gal4 line was provided by Frank Hirth, and <italic>D4</italic>-LacZ line by Ian Duncan.</p></sec><sec id="s4-3"><title>Immunostainings, cuticle preparation and in situ hybridization</title><p>Immunodetections in <italic>Drosophila</italic> embryos, imaginal discs, and cuticle preparations were performed according to standard procedures. <italic>Nematostella</italic> in situ hybridizations were performed as described (<xref ref-type="bibr" rid="bib23">Genikhovich and Technau, 2009</xref>). The antibodies used were: rat anti-HA (1/500; Molecular probe, Invitrogen, CA, USA), mouse anti-β-galactosidase (1/500; Molecular Probe), chicken anti-GFP (1/500; Promega, WI, USA), guinea pig anti-Homothorax (Natalia Azpiazu) and rabbit anti-HRP (1/100; FITC-conjugated, Jackson Immunoresearch, PA, US).</p></sec><sec id="s4-4"><title>BiFC analysis in <italic>Nematostella</italic> and <italic>Drosophila</italic> embryos</title><p>BiFC analysis in <italic>Drosophila</italic> embryos was performed as previously described (<xref ref-type="bibr" rid="bib28">Hudry et al., 2011</xref>). BiFC in <italic>Nematostella</italic> was achieved by injecting in vitro synthesized mRNAs. mRNAs synthesis was performed on a template produced by PCR using the mMessage mMachine T7 Kit (Ambion, Invitrogen, CA, USA). Embryos were co-injected with two BiFC vectors (50 ng/µl each) and fluorophore coupled-dextran. Embryos were allowed to develop for 24 hr and were processed for visualisation.</p></sec><sec id="s4-5"><title>Electro-mobility shift assays</title><p>Constructs for EMSAs were cloned in the pCDNA3 vector and sequence-verified before using. Proteins were produced with the TNT-T7-coupled in vitro transcription/translation system (Promega, WI, USA). Production yields of wild-type and mutated counterpart proteins were estimated by <sup>35</sup>S-methionine labelling. EMSAs were performed as described previously. We used the following double strands radiolabelled probes: <italic>Class I</italic> 5′-ACGCGGGAATGATTGATGGCCCAAATA, <italic>Meis-II</italic> 5′-ATGACAGCTCGGAATGATTAATGGCCCAAATA<italic>, Meis –IV</italic> 5′- ATGACAGCTCGGAATGATTAATTACCCAAATA <italic>a1a promoter</italic> 5′-TAATATTGTCAGTCAGATTGCAAATGATGATTGATCACTATAG, <italic>a7 promoter</italic> 5′-TAGGTCTGTCAGGCTGCTCTTTCACGATGATTTATTGCCTCAC, box2′ from the tsh epidermal enhancer <italic>tsh</italic> 5′-TCATGGACTGAAAACCATAAATTTGATAATTGACTTTCCAC (<xref ref-type="bibr" rid="bib44">McCormick et al., 1995</xref>), <italic>DllR</italic> 5′-TATTTGGGAAATTAAATCATTCCCGCGGACAGTT (<xref ref-type="bibr" rid="bib22">Gebelein et al., 2002</xref>), <italic>D4</italic><sup><italic>1–62</italic></sup> 5′-AGTTTACCATTAAATTCCCATTTAGGCTGTCAATCATTTGCGCTAATTTTTCTTGGCGGCTT (<xref ref-type="bibr" rid="bib15">Duncan et al., 2010</xref>), <italic>class IV</italic> 5′- ATGACAGCTCGGAATGATTAATTACCCAAATA, <italic>lab</italic><sup><italic>48/95</italic></sup> 5′-AAATTGATGGATTGCCCGGCGCCGACTGTCACCG (<xref ref-type="bibr" rid="bib53">Ryoo et al., 1999</xref>), and <italic>modC site I</italic> 5′-CCTCGTCCCACAGCTATAATGATTAATGAACGCGCCGCC (<xref ref-type="bibr" rid="bib33">Joshi et al., 2010</xref>). The sequence of all other probes (<italic>probes class II</italic> and <italic>III</italic>) is indicated in the corresponding figures. 1 mm of rat anti-HA (1/50; Molecular probe, Invitrogen, CA, USA) was used for the ‘super-shift’ experiments. Quantifications of shifted bands was performed using the Analyze&gt;Gels function of the ImageJ software.</p></sec><sec id="s4-6"><title>Bioinformatic analysis</title><p>By screening the literature two sets of 38 genes exclusively expressed in the endoderm or the ectoderm of <italic>Nematostella</italic> embryo could be identified. The density of the Pbx-Hox and Meis motifs in the <italic>cis</italic>-regulatory regions of these 72 genes was determined, using a previously established matrix (<xref ref-type="bibr" rid="bib63">Slattery et al., 2011</xref>). For more details, see the following website: <ext-link ext-link-type="uri" xlink:href="http://www.bigre.ulb.ac.be/Users/morgane/bruno/result.html">http://www.bigre.ulb.ac.be/Users/morgane/bruno/result.html</ext-link>.</p></sec><sec id="s4-7"><title><italic>Xenopus</italic> assays</title><p>One-cell stage <italic>Xenopus laevis</italic> embryos were microinjected with RNA encoding <italic>Nematostella vectensis</italic> Meis (NvMeis, 0.8 ng) protein. Animal Cap (AC) explants were removed from control and injected embryos at blastula stage and cultured to neurula stage 16. Total RNA was isolated from five control embryos (CE) and eighteen ACs from the control or injected groups. Semi-quantitative (sq) RT-PCR analysis was performed to posterior neural markers as described (<xref ref-type="bibr" rid="bib17">Elkouby et al., 2010</xref>). EF1alpha controls for RNA levels in each sample. RT-PCR was performed on total RNA from embryos.</p></sec></sec></body><back><ack id="ack"><title>Acknowledgements</title><p>We warmly thank Peter Holland, Michael Manuel, Michalis Averof, Vincent Laudet, and Abderrahman Khila for critical comments and Johanne Burden for proofreading the manuscript. We thank Jun Aruga, Ian Duncan, Natalia Azpiazu, Bruno Bello and the Bloomington stock centre for reagents and fly lines. We thank Yacine Graba for allowing us performing part of this work in his laboratory. Research in the author’s laboratory is supported by the CNRS, Ecole Normale Supérieure (ENS) of Lyon, EMBO short-term fellow (for B Hudry) and grants from ARC (Association de Recherche contre le Cancer) and FRM (Fondation pour la Recherche Médicale).</p></ack><sec sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>BH, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con2"><p>SM, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con3"><p>MT-C, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con4"><p>YV, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con5"><p>MD, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con6"><p>AD, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con7"><p>DF, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con8"><p>UT, Analysis and interpretation of data, Drafting or revising the article</p></fn></fn-group></sec><sec sec-type="supplementary-material"><title>Additional files</title><supplementary-material id="SD1-data"><object-id pub-id-type="doi">10.7554/eLife.01939.028</object-id><label>Supplementary file 1.</label><caption><p>Constructs generated for BiFC, functional and shift assays.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" 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pub-id-type="doi">10.1006/dbio.1999.9309</pub-id></element-citation></ref></ref-list></back><sub-article article-type="article-commentary" id="SA1"><front-stub><article-id pub-id-type="doi">10.7554/eLife.01939.029</article-id><title-group><article-title>Decision letter</article-title></title-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Tautz</surname><given-names>Diethard</given-names></name><role>Reviewing editor</role><aff><institution>Max Planck Institute for Evolutionary Biology</institution>, <country>Germany</country></aff></contrib></contrib-group></front-stub><body><boxed-text><p>eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see <ext-link ext-link-type="uri" xlink:href="http://elife.elifesciences.org/review-process">review process</ext-link>). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p></boxed-text><p>Thank you for sending your work entitled “Molecular insights into the origin of the Hox-TALE patterning system” for consideration at <italic>eLife</italic>. Your article has been favorably evaluated by a Senior editor and 3 reviewers, one of whom is a member of our Board of Reviewing Editors, and one of whom, David Ferrier, has agreed to reveal his identity.</p><p>The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission. </p><p>The comments below are a recombined text from the major comments provided by the three reviewers. All three support publication, but ask for some additional discussion and clarifications. This requires only modifications in the text, but no additional experiments. </p><p>The authors provide compelling functional evidence for a conservation of the Hox-TALE interaction network between Cnidaria and Bilateria. This is based on in vitro and vivo studies, including rescue constructs across taxa. They provide also negative evidence for some unclear homologs from lower taxa. The function of the Hox genes in cnidarians is a particularly contentious issue within the field and this manuscript represents an important new perspective on this debate, now supported with abundant new functional data. The detailed functional experiments performed here, involving two different <italic>Nematostella</italic> Hox genes clearly illustrate that this cnidarian has Hox (and Pbx and Meis) genes that function like the Hox genes of bilaterians, regardless of the difficulties of comparing the embryology and axial development of cnidarians relative to bilaterians. The variety in the modes of interaction between the Meis, Pbx and Hox proteins when the presence of a hexapeptide is varied is also of widespread interest, not just for the evolutionary implications highlighted in this manuscript, but also for the basic mechanistic implications for these transcription factors. </p><p>In conclusion, this paper provides some surprising results as to the functional conservation of Hox/PBC/Meis interactions. It tries to argue that the emergence of the HX motif in the superfamily has allowed a greater role for these proteins but it is difficult to see how the HX motif, as small as it is, could have evolved so many times. Yet, this represents a large amount of molecular and in vivo work that leads to the model that, by acquiring the ability to interact, the three protein classes have allowed the specification of positional information in animals. </p><p>There are, however, a few points that need additional discussion or a better placement in the relevant context: </p><p>1) The first difficulty relates to the orthology of Hox genes, or even their real nomenclature, which is difficult to assess in the absence of clustering and extensive sequence landmarks. However, the authors manage to define them as 'anterior' or more posterior. </p><p>2) The authors use BiFC extensively for defining protein–protein interactions, although it is not clear how specific these interactions might be. </p><p>3) The in silico search for mesodermal binding sites for Hox/Pbx (and Meis) is too biased and not terribly useful to show functional specificity. This only allows the definition of potential binding sites but the same data could have been obtained by using bona fide DNA sites. It is not clear what the authors are trying to say with these sites. </p><p>4) The more novel part of the paper concerns the extended Hox protein family, including NK proteins that also share an HX motif in higher animals. It is difficult to interpret the lack of direct interaction between Msx and PBC, likely due to the absence of an HX motif. However, the authors argue that the HX motif has appeared late in the superfamily of Hox proteins, but this is difficult to reconcile with the evolution of these families since this would imply that the HX domain has evolved independently in multiple proteins, after the duplication of the precursor Hox. </p><p>5) It seems that a bit more speculation would be warranted to place the work in context. For example, they do not touch the question of axis very much. In <xref ref-type="fig" rid="fig1">Figure 1</xref> they represent the aboral–oral axis of Cnidaria analogous to the anterior-posterior in bilateria. In the same figure they show evidence for asymmetry of Hox gene expression, along the directive axis, as it was also found by others. This would of course be in line with the enterocoel hypothesis and their short remark in the text would also support this. Hence, I would encourage them to add a paragraph on discussing axis homologies, although I do not expect that they can arrive at a final conclusion on this yet. Still, their work evidently contributes to this important question. </p><p>6) For the revisions, authors should revisit the question of which figures should be in the main text and which provide only supplementary information. </p></body></sub-article><sub-article article-type="reply" id="SA2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.01939.030</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p><italic>1) The first difficulty relates to the orthology of Hox genes, or even their real nomenclature, which is difficult to assess in the absence of clustering and extensive sequence landmarks. However, the authors manage to define them as 'anterior' or more posterior</italic>.</p><p>We agree there is a real difficulty in defining the orthology of cnidarian Hox genes. What is undisputed is the presence of anterior Hox genes. The others (in our terminology <italic>NvHoxE/F</italic>) are more difficult to place, as discussed in the first part of the result section. Another difficulty is the terminology of cnidarian Hox genes, which changes depending on the species and/or the authors. To be less confusing for non-cnidarian specialists, we now started the result section by providing a precise definition of the terminology and the possible orthology of <italic>Nematostella</italic> Hox genes. <xref ref-type="fig" rid="fig1">Figure 1</xref> was modified accordingly and now depicts the genomic organisation of <italic>Nematostella</italic> Hox genes with their corresponding groups of orthology. We also provided protein sequence alignments between <italic>Nematostella</italic> and <italic>Drosophila</italic> Hox proteins to better highlight the degree of conservation at the level of the HX- and HD-encompassing regions (<xref ref-type="fig" rid="fig2s3">Figure 2– figure supplement 3</xref> and <xref ref-type="fig" rid="fig2s4">Figure 2–figure supplement 4</xref>).</p><p><italic>2) The authors use BiFC extensively for defining protein–protein interactions, although it is not clear how specific these interactions might be</italic>.</p><p>Specificity of BiFC is a critical point, especially when considering that the complementary fragments of the fluorescent protein have a certain affinity, leading to a stabilization of the interactions between two candidate fusion proteins. Therefore it is important to have negative controls in hands, to confirm that BiFC signals are relevant of real protein–protein interactions in vivo. We already described all suitable negative controls in <italic>Drosophila</italic>, mammalian cells and chick embryos (Hudry et al., BMC Biology 2011; Hudry et al., PLOS Biology 2012). These negative controls were repeated in our experiments with <italic>Nematostella</italic> fusion proteins. In particular, we showed that each individual sub-fragment of the Venus protein could not interact with the complementary fragment fused to <italic>Nv</italic>Pbx or <italic>Nv</italic>Meis (<xref ref-type="fig" rid="fig3">Figure 3B</xref>). This is now more clearly stated in the Result section: “No BiFC was obtained between a fusion construct and the complementary isolated VC or VN fragment, highlighting that the interaction between <italic>Nv</italic>Pbx and <italic>Nv</italic>Meis fusion proteins was not artificially induced by the inherent affinity of the VN and VC fragments (<xref ref-type="fig" rid="fig3">Figure 3B</xref>)”. Along the same line we provided evidence that BiFC cannot occur in conditions where Hox-PBC interactions are abolished (with the DNA-binding deficient form of <italic>Nv</italic>Pbx: <xref ref-type="fig" rid="fig3">Figure 3C</xref>).</p><p><italic>3) The in silico search for mesodermal binding sites for Hox/Pbx (and Meis) is too biased and not terribly useful to show functional specificity. This only allows the definition of potential binding sites but the same data could have been obtained by using bona fide DNA sites. It is not clear what the authors are trying to say with these sites</italic>.</p><p>We have now described more precisely the logic behind the search for <italic>Nematostella</italic> Hox/TALE binding sites in the genome: “Our band shift assays were performed on consensus binding sites previously defined with bilaterian Hox and TALE proteins. To know whether such sites could be used in the context of <italic>Nematostella</italic> development, we searched for their presence in the <italic>Nematostella</italic> genome.”</p><p><italic>4) The more novel part of the paper concerns the extended Hox protein family, including NK proteins that also share an HX motif in higher animals. It is difficult to interpret the lack of direct interaction between Msx and PBC, likely due to the absence of an HX motif. However, the authors argue that the HX motif has appeared late in the superfamily of Hox proteins, but this is difficult to reconcile with the evolution of these families since this would imply that the HX domain has evolved independently in multiple proteins, after the duplication of the precursor Hox</italic>.</p><p>This comment can be addressed with the minor comments from Reviewer 2. He/she proposes the exact opposite: “In the context of the discussion, I wonder whether it really is so difficult to imagine that the hexapeptide evolved independently in distinct ANTP subclasses? It is, after all, a short sequence in which a high degree of variability can be seen amongst gene families and between taxa. In some instances it seems to effectively be just a single Tryptophan (W) residue. One scenario might be that once a hexapeptide–TALE interaction is established in one family then the hexapeptide-interacting aspect of the TALE protein is established and is retained whilst the hexapeptide evolves in other ANTP subclasses? This scenario is the compliment of the differential loss scenario described by the authors, in terms of explaining the patchy distribution of hexapeptide domains across the ANTP class.”</p><p>Here we presented two possible scenarios, taking into account the phylogeny history of ANTP class genes. In both models, we postulated that the HX was present in a common ancestor of Hox, NK and extended-Hox members. We did not argue that the HX appeared late in Hox proteins. We agree with Reviewer 2 that given the short size of the HX, this motif could have appeared independently in multiple times during evolution. However, we have to consider that this motif is always located at a precise position in all ANTP subclass members (upstream of the HD), which is probably important to ensure interactions with PBC members. Along the same line, the distance between the HX and the HD may also have played important roles in the acquisition of new functions, as noticed in certain bilaterian Hox proteins. For all these reasons, it is difficult to imagine that the invariant position of the HX could result from independent acquisitions during metazoan evolution. We tried to better emphasize this point in the corresponding discussion part.</p><p><italic>5) It seems that a bit more speculation would be warranted to place the work in context. For example, they do not touch the question of axis very much. In</italic> <xref ref-type="fig" rid="fig1"><italic>Figure 1</italic></xref> <italic>they represent the aboral-oral axis of Cnidaria analogous to the anterior-posterior in bilateria. In the same figure they show evidence for asymmetry of Hox gene expression, along the directive axis, as it was also found by others. This would of course be in line with the enterocoel hypothesis and their short remark in the text would also support this. Hence, I would encourage them to add a paragraph on discussing axis homologies, although I do not expect that they</italic> can <italic>arrive at a final conclusion on this yet. Still, their work evidently contributes to this important question</italic>.</p><p>We chose not to extrapolate too much with our results on the longstanding and heavy debate of the homologous comparison between bilaterian and cnidarian longitudinal axes. We have now discussed this point in more detail, providing references illustrating the controversy for both the primary and secondary axes of cnidarians. We concluded on the fact that patterning molecules (Hox, BMPs, etc) could simply be used along different longitudinal axes in different species. What is important is the existence of a patterning system that could be co-opted during evolution: “Together these observations highlight that patterning molecules can be used along different longitudinal axes during animal evolution, which renders difficult the comparison between Bilateria and Cnidaria. Here we propose that the ancestral molecular cues underlying the Hox patterning system along the cnidarian directive axis could have been recruited for AP patterning in Bilateria.”</p><p><italic>6) For the revisions, authors should revisit the question of which figures should be in the main text and which provide only supplementary information</italic>.</p><p>We have changed the previous supplementary figures 9 and 11-13 into <xref ref-type="fig" rid="fig7 fig9">Figures 7 and 9</xref>, respectively. In addition, we have simplified the presentation of previous <xref ref-type="fig" rid="fig6 fig7">Figures 6 and 7</xref>, which are now regrouped in a new <xref ref-type="fig" rid="fig6">Figure 6</xref>, focusing on functional data in <italic>Drosophila</italic>. Preliminary in vivo and in vitro interaction assays are now included in figure supplements.</p></body></sub-article></article>