abdominal-A

A central question is how the homeotic proteins achieve theirdevelopmental specificity despite the very similar DNA binding specificities of isolated homeoticproteins in vitro. Specificity could be achieved by differential interactions with protein cofactors.The extradenticle gene might encode such a cofactor since it interacts genetically in parallel with Ultrabithorax, abdominal-A, and perhaps other homeotic genes. There is a selective interaction of the Extradenticle homeodomain protein with certain Ultrabithorax and Abdominal-A proteins but not with an Antennapedia protein or a more distant homeodomain protein (Johnson, 1995).

Extradenticle protein modulates the morphological consequences of homeotic selector genes. Extradenticle proteinraises the DNA binding specificity of Ultrabithorax and Abdominal-A but not that of Abdominal-B.Extradenticle modulates the DNA binding activity of Engrailed to a differenttarget site. While a region N-terminal of the Extradenticle homeodomain is required forUltrabithorax and Abdominal-A cooperativity, Engrailed requires a domain C-terminal of the Extradenticle homeobox (van Dijk, 1994).

UBX, ABD-A and ANTP differentially regulate the Antennapedia P1 promoter in a cell culture cotransfection assay: UBX and ABD-A repress, whereas ANTP activates P1. Either of two regions of P1 canconfer this pattern of differential regulation (Saffman, 1994).

The homeobox gene extradenticle (exd) acts as a cofactor of Hox function in both Drosophila and vertebrates. It has been shown that the distribution of the Exd protein is developmentally regulated at the post-translational level; in the regions where exd is not functional, Exd is present only in the cell cytoplasm, whereas it accumulates in the nuclei of cells requiring exd function. Maternal EXD mRNA lasts for a few hours and is undetectable by stage 9 of embryogenesis. Protein produced by maternal RNA is stable. Both maternally and zygotically derived protein translocates into nuclei, suggesting that the proteins translocated from both mRNAs are functional and also suggesting that regulation of protein distribution is not dependent on transcriptional control (Azpiazu, 1998).

The subcellular localization of Exd is regulated by the BX-C genes; to varying degrees, BX-C genes can prevent or reduce nuclear translocation of Exd. Embryos homozygous for the deficiency Df(3R)P9, lacking the entire Bithorax complex, contain Exd at high levels in the nuclei of epidermal cells of both thoracic and abdominal segments. Only in the Keilin's organs of each segment does Exd remain cytoplasmic. This rise in the level of nuclear Exd in the abdominal segments (in comparison with the wild-type distribution) already indicates an involvement of the BX-C genes with the subcellular distribution of the product. In contrast, the thorax-determining genes Sex combs reduced (Scr) and Antp do not appear to affect Exd localization, as Scr Antp homozygous embryos exhibit normal distribution of Exd. To discriminate the roles of individual BX-C genes in the nuclear translocation of Exd, the distribution of Exd protein was examined in two more BX-C mutant combinations: Ubx- abd-A+ Abd-B+ and Ubx- abd-A- Abd-B+. Embryos homozygous for the first combination, defective only for Ubx function, show an increased level of nuclear Exd in the first abdominal segment as compared to wild type. In more posterior abdominal segments the levels and distributions of Exd are normal. In the second combination, lacking Ubx and abd-A functions, Exd is detected at high levels in the nuclei of the abdominal segments A1 to A4. In Df(3R)P9 (Ubx abd-A Abd-B) embryos, Exd nuclear localization extends to A8: all these results indicate that each BX-C gene is capable of preventing or reducing the nuclear translocation of Exd (Azpiazu, 1998).

The inhibition of Exd nuclear transport by overexpression of BX-C genes causes exd-like phenotypes. This was shown by inducing ectopic Ubx expression with several Gal4 lines during embryonic development and examining the segmental transformations produced. In the presence of normal exd function, Ubx specifies the pattern of the first abdominal (Al) segment. In contrast, in embryos lacking exd function, Ubx specifies a pattern resembling a more posterior segment, of A3-A5 type. Under conditions in which levels of Gal4 activity are high, larvae develop all segments anterior to A2 with an A3-A5 pattern. This segment pattern closely resembles that found in the A1 segment of zygotic exd larvae and is the same overall pattern observed after heat shock-inducing Ubx expression in zygotic exd embryos. These observations indicate that high levels of Ubx protein are able to produce an exd-like phenotype, in good agreement with the observed negative effect of BX-C genes on the nuclear translocation of Exd (Azpiazu, 1998).

Mutations in homothorax (also known as dorsotonals), which codes for a protein that interacts with Extradenticle, seem to alter the identity of the abdominal chordotonal neurons, which depend on Abd-A for their normal development. However, these mutations do not alter the expression of the abd-A gene, suggesting that hth may be involved in modulating abd-A activity. In wild-type embryos, the LCh5 neurons are located invariably in the lateral PNS cluster of abdominal segments A1-A7. In contrast, these neurons are situated in a more dorsal position in (respectively) either 25% or 36% of the abdominal segment in the PNS of embryos homozygous for hth H321 (n=91) or hth J186 (n=56). The affected Ch neurons remain associated with the dorsal PNS cluster, or occasionally, are positioned between the dorsal and lateral PNS clusters. The orientation of the affected neurons is also abnormal. Whenever the affected LCh5 neurons remain associated with the dorsal PNS cluster, their dendrites point ventrally or posteriorly instead of dorsally. The 'dorsal chordotonals' phenotype can be detected in all the abdominal segments in varying frequencies. In weak alleles, it is observed more frequently in the posterior abdominal segments (A5-A7). Stronger alleles affect all the abdominal segments in similar frequencies. Weak hth alleles do not affect any PNS neurons other than the LCh5 neurons. Strong hypomorphic mutations in hth affect not only the position and orientation of the LCh5 neurons, but also cause a reduction in their number. Only three dorsal Ch neurons are observed in nearly 100% of abdominal segments of mutants for strong alleles. Most of the affected neurons remain associated with the dorsal PNS cluster; their dendrites point ventrally. In spite of their abnormal location and orientation, the affected Ch neurons appear fully differentiated, as judged by their overall morphology and the presence of normal-looking scolopales at the tips of their dendrites. The precursors of the LCh5 neurons are born in a normal dorso-lateral position in hth mutant embryos. In the dorsal cluster one dorsal ES neuron and 2-3 Cut-negative MD neurons are lost. The ventral Ch neurons are only rarely lost in strong mutants (Kurant, 1998).

A similar phenotype was observed in embryos homozygous for mutations in the homeotic selector gene abd-A. In the absence of abd-A activity, the LCh5 neurons are transformed into DCh3 neurons, and as such they remain associated with the dorsal PNS cluster and their dendrites pointed ventrally. Since the PNS phenotype associated with loss of hth function suggests a homeotic transformation of LCh5 neurons towards the identity of DCh3 or A8-LCh3 neurons, which do not depend on abd-A for their development, the expression pattern of the Abd-A protein was examined in hth mutant embryos. Abd-A is normally expressed in the ectoderm of abdominal segments from PS7 to the anterior region of PS13. In addition, Abd-A is expressed in the LCh5 neurons of segments A1-A7 and in the VNC in segments A2-A7. The spatial distribution of the Abd-A protein is not altered in the ectoderm or CNS of embryos homozygous for the hth K1-8 allele as compared to wild-type embryos, although a slight reduction in the level of the protein is observed. It is concluded that hth may be required for the activity of Abd-A, rather than its expression. A similar dorsal chordotonal phenotype is found in extradenticle mutants (Kurant, 1998)

Why do the LCh5 neurons remain dorsal in the absence of hth activity? Although the process of Ch organ migration and rotation is not understood, the system can be divided conceptually into two components: the neuronal cells and their environment (or the receiving and signaling components of the pathway, respectively). Two scenarios can be envisioned that are not mutual exclusive. One is that hth affects the homeotic identity of the LCh5 neurons themselves. The other possibility is that hth affects the environment in which these neurons form and migrate. In midgut development abd-A andUbx, which are expressed in neighboring parasegments of the visceral mesoderm, regulate dpp and wingless expression, which affects the underlying endoderm. It is possible that the influence of HTH and EXD on Abd-A activity in the ectoderm affects signaling molecules such as Wingless and DPP, which in turn affect the localization of the Ch neurons (Kurant, 1998).

The hexapeptide and linker regions of the AbdA hox protein regulate its activating and repressive functions

The Hox family transcription factors control diversified morphogenesis during development and evolution. They function in concert with Pbc cofactor proteins. Pbc proteins bind the Hox hexapeptide (HX) motif and are thereby thought to confer DNA binding specificity. The mutation of the AbdA HX motif as reported here does not alter its binding site selection but does modify its transregulatory properties in a gene-specific manner in vivo. A short, evolutionarily conserved motif, PFER, in the homeodomain-HX linker region acts together with the HX to control an AbdA activation/repression switch. These in vivo data thus reveal functions not previously anticipated from in vitro analyses for the hexapeptide motif in the regulation of Hox activity (Merabet, 2003).

Hox proteins share a helix-turn-helix DNA binding motif, the homeodomain (HD), and, consequently, recognize very similar TAAT core sequences; this fact contrasts with the highly specific biological functions carried out by Hox proteins during development. It is now well established that Hox proteins gain specificity by physically interacting with Pbc class cofactors. Association with Pbc proteins increases the DNA binding specificity of Hox proteins: Hox/Pbc complexes recognize a larger motif, TGATNNATNN, where the identity of the central NN nucleotides depends on the particular Hox protein involved (Merabet, 2003).

Hox/Pbc interactions are now well characterized in vitro, both in biochemical and structural terms. Pbc proteins belong to the TALE (three amino acid loop extension) class of atypical HD-containing proteins that is characterized by a three amino acid insertion between helices 1 and 2 of the HD. These residues participate in the constitution of a hydrophobic pocket that mediates interaction with Hox proteins, through a short evolutionary conserved sequence, the hexapeptide (HX), lying upstream of the HD in all but the Abdominal-B class of Hox proteins. Structurally, the HX folds into a classical type I reverse turn and is connected to the HD by a short sequence commonly termed the linker region. The variable length and disordered structure of the linker region suggest that it has a passive role in connecting the HX to the HD (Merabet, 2003).

In vitro, the HX promotes the formation of Hox/Pbc complexes with heightened DNA binding affinity and specificity, suggesting that this domain critically contributes to the selection of Hox target genes during development. The role of the HX in vivo has, however, been poorly investigated so far. One study has addressed the point by analyzing in Drosophila the effect of the HX-mutated Labial (Lab) protein on the regulation of a heterologous mouse Hoxb1 enhancer, 3Xrpt3 (Popperl, 1995). The authors concluded that the recruitment of Extradenticle (Exd) by the HX neutralizes an inhibitory effect of the HX on Lab DNA binding. This might, however, be a very specialized function of the HX, since Lab is very peculiar in the sense that, unlike most Hox proteins, it does not bind DNA on its own (Merabet, 2003 and references therein).

A detailed analysis has been carried out of the HX function in the regulation of bona fide target genes during development. To address the contribution of the HX and the linker region, two variants were generated, AbdA(HXm) and AbdA(PFERm), where the YPWM motif and the PFER sequence were mutated into AAAA. PFER lies in the middle of the AbdA linker region, which has been fairly well conserved in the insect phylum. The HX is not involved in controlling DNA binding and target gene selection, nor is it necessary for Exd recruitment, but, rather, it controls transregulatory functions of the Hox protein Abdominal-A (AbdA). An evolutionarily conserved motif in the linker region interferes with the HX, to control a repression/activation switch in AbdA (Merabet, 2003).

Extensive in vitro analyses have demonstrated that the HX is responsible for the interaction with Pbc proteins, leading to the view that this motif imparts Hox DNA binding specificity and therefore assists Hox proteins in the selection of appropriate target genes. In vivo data challenge this view in several ways. (1) The unaltered capacity of AbdA(HXm) to induce A2-like identities in the thorax and to form dimeric complexes on DNA with Exd shows that the HX is not the only motif of AbdA that is able to recruit Exd. A similar situation has been shown to occur in Ubx, indicating that other residues in Hox proteins can compensate for the lack of the HX in mediating Hox/Exd interactions. (2) Mutation of the HX does not affect binding site selection by AbdA, as shown by the ability of the mutant protein to bind target sequences from Dll and dpp in vitro, and to control dpp promoter elements in vivo. Accordingly, the HX mutation does not alter target gene selection (in this case, wg and dpp in the VM) in vivo. (3) The fact that the HX mutation modifies AbdA function in the regulation of dpp, which does not depend on Exd, implies that the HX should interact with additional proteins that remain to be identified. These data thus endow the HX with unexpected functions; this does not preclude that the HX could, however, play a role in target selection in other developmental contexts. The PFER motif within the linker region was found to fulfill an important regulatory function; this was also unexpected, considering the variable length and disordered structure of this region (Merabet, 2003).

The regulation of dpp by AbdA in the VM is mediated by the dpp674 enhancer, which contains seven binding sites for AbdA. Sites 1-4 in dpp419 (the 3' portion of dpp674) mediate repression by AbdA, while sites 5-7 in dpp265 (the 5' portion of dpp674) mediate activation. Interestingly, dpp265 reveals an activating potential of AbdA on dpp transcription that is masked by the prevalence of repression over activation in the regulation of dpp674 or dpp. Exd acts in a Hox-independent manner to repress dpp in the anterior VM. Anterior expression of dpp induced by AbdA(HXm) could therefore result from an interference with the repressive function of Exd, rather than from a direct effect on dpp transcription. However, while dpp265 is not derepressed anteriorly in exd- or hth-deficient animals and, therefore, does not contain the sequences mediating repression by Exd, it is activated by AbdA(HXm). Thus, Exd and AbdA(HXm) act on different regulatory sequences to respectively repress or activate dpp in the anterior VM, which makes it unlikely that activation by AbdA(HXm) results from an interference with the Hox-independent repressive function of Exd. Considering that the HX mutation affects neither DNA binding nor target site recognition in vitro and in vivo, it is proposed that AbdA(HXm), as does AbdA, controls dpp transcription directly (Merabet, 2003).

The function of the HX and PFER motifs in switching AbdA from an activator to a repressor clearly depends on the cis-regulatory target sequence, which is illustrated by the distinct effects of the variants on dpp and wg transcription, and of AbdA(PFERm) on dpp419 and dpp265. Taking these observations together, a model is proposed that accounts for how the distinct regulatory modules, which have been identified functionally, interconnect to specify AbdA activity in the VM. According to this model, the HX plays a central dual role in repressing the function of a Q-rich activation domain and promoting that of a repression domain whose location remains to be determined. For the regulation of dpp, the HX senses dpp cis-regulatory specificity to select the repressive potential of AbdA. Conversely, in the regulation of wg, the PFER sequence senses wg cis-regulatory specificity to select the activating potential of the Hox protein. According to the functional epistatic relationship between the two motifs, suggested by the activity of the doubly mutated AbdA(HXm;PFERm) variant, the PFER sequence would not directly control repressive or activating domains of AbdA but, rather, acts upstream, as an inhibitor of HX function (Merabet, 2003).

This study demonstrates unappreciated regulatory functions for the HX and for the linker region, both acting together as a platform, sensing cis-regulatory specificity to ultimately select the activating or repressing potential of AbdA. Results from other studies suggest that conclusions from these in vivo experiments could be extended to Hox factors other than AbdA: (1) this model emphasizes the importance of the cis-regulatory context for the control of AbdA activity, consistent with the dependency of the transactivating potential of vertebrate Hox proteins on the DNA binding context; (2) the functional importance of the linker region is also suggested by the finding that a phosphorylated residue lying between the HX and the HD is critical for mouse Hoxb7-mediated inhibition of granulocytic differentiation, and most important, (3) a recent report also identified the linker region as playing a DNA binding-independent role in Ubx-mediated repression of Dll (Merabet, 2003).

Finally, these observations might also be relevant for mechanisms that relate molecular changes in Hox proteins to changes in morphology during animal evolution. The HX has been proposed to play a major role in conferring homeotic character to HD-containing proteins, as suggested by the simultaneous loss of homeotic function and HX motif in the Drosophila pair-rule Fushi-tarazu protein. These observations suggest that the acquisition of novel developmental properties by HD proteins during evolution presumably relies not only on changes in DNA binding specificity, but also on changes in transregulatory properties. In this context, modifying the regulation of only a subset of Hox targets while leaving others unchanged, by gain or loss of regulatory modules such as the HX and PFER motifs, might provide evolutionary advantages and be causal in morphological diversification. The importance of a tight control of Hox transregulatory properties in evolution has recently gained further support from the evolving capacity of Ubx in controlling the repression of Dll in the insect phylum (Merabet, 2003 and references therein).

Competition for cofactor-dependent DNA binding underlies Hox phenotypic suppression

Hox transcription factors exhibit an evolutionarily conserved functional hierarchy, termed phenotypic suppression, in which the activity of posterior Hox proteins dominates over more anterior Hox proteins. Using directly regulated Hox targeted reporter genes in Drosophila, this study shows that posterior Hox proteins suppress the activities of anterior ones by competing for cofactor-dependent DNA binding. Furthermore, a motif in the posterior Hox protein Abdominal-A (AbdA) was identified that is required for phenotypic suppression and facilitates cooperative DNA binding with the Hox cofactor Extradenticle (Exd). Together, these results suggest that Hox-specific motifs endow posterior Hox proteins with the ability to dominate over more anterior ones via a cofactor-dependent DNA-binding mechanism (Noro, 2011).

fkh250 is a 37-base-pair (bp) element from the forkhead (fkh) gene, which is directly regulated by Scr; it contains a single Hox-Exd-binding site that, compared with other Hox-Exd heterodimers, is preferentially bound by Scr-Exd in vitro (Ryoo, 1999). When lacZ is placed under the control of fkh250, fkh250-lacZ is specifically expressed in PS2 in an exd- and Scr-dependent manner. Indeed, misexpression of Scr throughout the Drosophila embryo can ectopically activate fkh250-lacZ. Notably, ectopic activation of fkh250-lacZ occurs even in the abdomen, in the presence of endogenous, more posterior Hox (Noro, 2011).

In contrast to fkh250, fkh250^CON (for 'consensus') is an artificial variant of fkh250 with two base pair substitutions that enable fkh250^CON-lacZ to be directly regulated by four Hox genes in an exd-dependent manner: Scr, Antp, and Ubx activate this reporter in PS2-PS6, while AbdA represses it in abdominal segments (Ryoo, 1999). Consistent with its relaxed specificity in vivo, fkh250^CON binds well to Scr-Exd, Antp-Exd, Ubx-Exd, and AbdA-Exd heterodimers in vitro. The promiscuous binding and regulation by multiple Hox proteins classifies fkh250^CON as a shared Hox target gene, while the Scr-specific regulation of and binding to fkh250 suggests that it is a specific Hox target gene (Mann, 2009; Noro, 2011).

Because of their distinct specificities, fkh250-lacZ and fkh250^CON-lacZ provide an ideal system to examine the molecular mechanism of phenotypic suppression. In accordance with the premise of posterior dominance, coexpression of Scr and AbdA throughout the fly embryo leads to repression of fkh250^CON-lacZ by AbdA. Note that both fkh250 and fkh250^CON-lacZ require direct binding by the Hox cofactor Exd. The primary distinction between these two readouts is that AbdA-Exd binds well to fkh250^CON but not to fkh250. Accordingly, it is concluded that AbdA cannot suppress the activities of Scr if it cannot bind to the target element. Furthermore, in this system, posterior dominance cannot be mediated by miR activity or competition for factors, such as Exd, off DNA. Rather, these data support a model in which competition for cofactor-dependent DNA binding underlies phenotypic suppression for shared Hox target genes (Noro, 2011).

If AbdA is outcompeting Scr for binding to fkh250^CON, AbdA would be expected to have a higher affinity for this sequence compared with Scr. To test this prediction, the affinities of AbdA-Exd and Scr-Exd heterodimers for fkh250^CON were measured in vitro. AbdA-Exd heterodimers bound more than twofold more tightly to fkh250^CON compared with Scr-Exd. Thus, at the same concentration, AbdA-Exd is more likely than Scr-Exd to be bound to fkh250^CON, consistent with the idea that competition depends on cofactor-dependent DNA binding (Noro, 2011).

Binding to fkh250^CON is Exd-dependent for both AbdA and Scr, implying that AbdA has domains that allow higher binding affinity with Exd to this target site. In general, Hox interactions with Exd are mediated by the highly conserved, four-amino-acid motif YPWM, which directly binds to a hydrophobic pocket established by the three-amino-acid loop extension (TALE) in the Exd homeodomain (Mann, 2009). For some Hox proteins, the YPWM-TALE interaction is necessary and sufficient for cooperative DNA binding with Exd and target gene regulation in vivo (Joshi, 2010). In addition to the YPWM motif, AbdA, but not Scr, has a second well-conserved tryptophan-containing motif, TDWM, which could play a role in mediating AbdA-Exd interactions. However, when a mutant form of AbdA in which both the YPWM and TDWM motifs are mutated to alanines (2W^Ala) was coexpressed with Scr in the phenotypic suppression assay, fkh250^CON-lacZ was repressed to the same extent as by wild-type AbdA. Thus, although the YPWM and TDWM may contribute to interactions with Exd, these motifs are not necessary for AbdA to dominate over Scr (Noro, 2011).

Immediately C-terminal to its homeodomain, AbdA contains a so-called UbdA motif, a nine-amino-acid sequence also present in Ubx, which has been suggested to mediate cooperative binding with Exd to some DNA sequences (Merabet, 2007). In fact, UbdA is part of a larger 23-residue conserved region adjacent to the AbdA homeodomain, which is referred to as the UR motif (for UbdA-RRDR). To determine whether this or other regions in the C-tail of AbdA are involved in mediating phenotypic suppression, a series of C-terminal truncations were tested for their ability to compete with Scr for the repression of fkh250^CON-lacZ in vivo. All AbdA variants were epitope-tagged, allowing use of transgenes that express at similar levels (Noro, 2011).

AbdA's ability to compete with Scr for fkh250^CON regulation is eliminated when the entire C terminus is removed (ΔC¹⁹⁷). Adding back only the UR motif partially restores AbdA's ability to dominate over Scr (ΔC²²⁰). Consistently, an internal deletion that removes most of the UR motif (Δ^200-220) exhibits a reduced ability to repress fkh250^CON-lacZ. No additional loss of repressive activity is displayed by an AbdA variant in which both the YPWM and TDWM motifs are mutated in combination with this internal deletion (2W^AlaΔ^200-220). Additional sequences in the C-tail of AbdA may account for the residual activity of variants lacking the UR motif (Δ^200-220 and 2W^AlaΔ^200-220). All AbdA variants used in this study are capable of repressing the exd-independent target gene spalt in the wing imaginal disc, confirming that these mutants are still functional transcription factors. Furthermore, these mutants retain the ability to repress gene expression in vivo, arguing that AbdA's repressive activity is not sufficient to account for its ability to dominate Scr. Together, these data highlight the importance of the UR motif for phenotypic suppression (Noro, 2011).

The above data show that the UR motif is required for AbdA to compete with Scr in vivo. To test the hypothesis that UR carries out this function by facilitating cooperative DNA binding with Exd, the ability of the truncated AbdA variants to bind fkh250^CON in complex with Exd was analyzed. In general, the results correlate with the in vivo phenotypic suppression assay: Those mutants that failed to suppress Scr's ability to activate fkh250^CON-lacZ (ΔC¹⁹⁷, Δ^200-220, and 2W^AlaΔ^200-220) were severely compromised in binding fkh250^CON with Exd in vitro. Together, these data strongly suggest that cooperative DNA binding with Exd is required for phenotypic suppression and that domains unique to AbdA are critical for its ability to dominate over Scr. More specifically, they argue that AbdA's UR motif is necessary for cooperative binding of AbdA and Exd to fkh250^CON and that the YPWM and TDWM motifs are not sufficient to mediate this interaction on this binding site. The insufficiency of the YPWM motifs to mediate cooperative binding with Exd has been observed for other Hox proteins, suggesting that the use of paralog-specific motifs such as UR may be a general phenomenon (Noro, 2011).

To test the generality of AbdA's dependency on its UR motif for posterior dominance, the same AbdA variants were analyzed for their ability to suppress the activity of the thoracic Hox protein Antp in the patterning of the larval epidermis. When ectopically expressed, Antp transforms the head and first thoracic segment (T1) toward the identity of the second thoracic segment (T2), where Antp is normally expressed). In contrast, when AbdA is ectopically expressed, the head and thorax acquire abdominal segmental identities. Consistent with the rules of phenotypic suppression, wild-type AbdA is able to produce this transformation even in the presence of exogenous Antp. However, similar to the results with fkh250^CON-lacZ, AbdA mutants that are compromised in their ability to cooperatively bind DNA with Exd (e.g., ΔC¹⁹⁷, Δ^200-220, and 2W^AlaΔ^200-220) fail to suppress the activity of Antp (Noro, 2011).

Taken together, these data support a model in which phenotypic suppression depends on a competition for cofactor-dependent DNA binding. It follows that this mechanism would only apply to readouts that depend on regulatory elements that are targeted by multiple Hox proteins. For example, ectopic Scr can activate fkh and other target genes required for salivary gland development in more posterior segments, illustrating that this Hox-specific function does not obey phenotypic suppression. Furthermore, it is particularly noteworthy that, compared with the anterior Hox protein Scr, AbdA has additional motifs that facilitate complex formation with Exd on DNA. These data suggest that when phenotypic suppression is observed, the more posterior Hox proteins may have a higher affinity for shared binding sites; this higher affinity is a consequence of the quantity and quality of motifs that mediate cooperative DNA binding with Exd. It is speculated that these motifs may be used differently at different target genes and binding sites. It is suggested that the YPWM motif provides a common, basal level of interaction between Hox proteins and Exd. In the context of Hox-specific regulatory elements, this motif may be sufficient to enable Hox-Exd regulation of some target genes. In contrast, in the context of shared enhancers and when multiple Hox proteins are coexpressed, additional, paralog-specific motifs present in the more posterior Hox proteins enable tighter binding of Hox-Exd dimers to DNA, leading to more posterior phenotypes. This was shown to be the case for a single shared Hox-Exd enhancer and suggest that the generality of this mechanism for phenotypic suppression will become apparent as more shared and specific targets for Hox proteins are characterized at high resolution (Noro, 2011).

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