Protein degradation is a key regulator of the cell cycle, inflammation and transcription — but little is known about its role in development. Zhu and Kirschner now report in Developmental Cell the identification of Xom — a developmental gene that is regulated by proteolysis.

In a screen to identify gene products that are differentially degraded before and after the onset of midblastula transition, the authors found that two proteins matched these criteria: an unknown protein and Xom, a homeobox transcription factor, which was stable during early gastrulation but subsequently degraded. Further experiments showed that Xom's degradation depended on the ubiquitin–proteasome pathway.

It turned out that one of two PEST domains (proline-, glutamic acid- and aspartic acid-, serine- or threonine-rich regions) present in Xom was required for Xom degradation. Interestingly, this so-called 'Xom destruction motif' (XDM) resembles the glycogen synthase kinase 3 (GSK3) consensus phosphorylation site, which is conserved in the known substrates for GSK3-dependent proteolysis such as β-catenin.

Within the XDM, the authors found two phosphorylation sites — Ser140 and Ser144. A peptide of the phosphorylated XDM blocked Xom degradation. Paradoxically so did the unphosphorylated peptide, implying that the embryonic extract used in these assays contained a kinase activity, although this turned out not to be GSK3. By contrast, the same peptide in which Ser140 and Ser144 were mutated to Alanine residues was unable to block Xom degradation.

Using in vitro binding assays, Zhu and Kirschner found that the E3 ubiquitin ligase Skp1–Cullin–F-box complex (SCF) containing the F-box protein βTRCP is responsible for Xom degradation. And they were able to show that a dominant-negative βTRCP mutation blocked Xom degradation in vivo. Intriguingly, this E3 ubiquitin ligase complex also mediates the phosphorylation-dependent degradation of β-catenin.

So, what is the role of Xom degradation in early Xenopus development? Bone-morphogenetic protein 4 (BMP4) is a ventral morphogen that acts together with Xom in an auto-activating feedback loop — Xom is activated by BMP and vice versa. In addition, Xom inhibits the transcriptional activity of dorsal-specific genes that, in turn, inhibit BMP activity. Zhu and Kirschner hypothesized that proteolysis of Xom might be needed to cease Xom-mediated repression of dorsal-specific genes such as goosecoid during early gastrulation. If true, the auto-activating circuit would be eliminated, leading to dorso–ventral asymmetry in the mesoderm, and loss of BMP expression on the dorsal side and high expression on the ventral side.

Indeed, luciferase reporter assays showed that non-degradable Xom is about 20 times better at inhibiting transcriptional activation of goosecoid than wild-type Xom. Consistent with this, embryos with non-degradable Xom have head truncation — typical of an enhanced ventralized phenotype — and this effect is restricted to the dorsal site of the embryos.

On the basis of these findings, Zhu and Kirschner propose that correct dorso–ventral BMP patterning in the mesoderm during gastrulation depends on specifically timed proteolysis of Xom. It is currently unclear how Xom is stabilized in the early gastrulation stage and what turns on Xom degradation later in gastrulation.