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, in Xenopus, to identify gene products that are differentially degraded before and after the onset of midblastula transition, the authors found two proteins that matched these criteria — an unknown protein and Xom, a homeobox transcription factor. Xom is stable during early gastrulation but is subsequently degraded through the ubiquitin–proteasome pathway.

Xom has two so-called PEST domains (proline, aspartate and glutamate, serine, or threonine-rich regions), one of which turned out to be 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 of GSK3-dependent proteolysis, such as β-catenin.

In the XDM, the authors found two phosphorylation sites at Ser140 and Ser144. In an in vitro assay, an exogenous peptide of the phosphorylated XDM blocked Xom degradation, paradoxically so did the unphosphorylated peptide. However, phosphorylation of XDM seems to be important for Xom degradation because the same peptide, when it contains serine-to-alanine mutations at positions 140 and 144, cannot block Xom degradation in vitro, implying that the embryonic extract used in these assays contained a kinase activity, although this turned out not to be GSK3.

Using in vitro binding assays, Zhu and Kirschner next found that the E3 ubiquitin ligase Skp1–Cullin–F-box complex (SCF), which contains the F-box protein β-TRCP, is responsible for Xom degradation. And they were able to show that a dominant-negative form of β-TRCP could block Xom degradation in vivo. Intriguingly, the same 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? BMP4 is a ventral morphogen that acts together with Xom in an auto-activating feedback loop in which Xom is activated by BMP and vice versa. In addition, Xom inhibits transcriptional activity of dorsal-specific genes that, in turn, inhibit BMP activity. Zhu and Kirschner hypothesize that the 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 dorsoventral asymmetry in the mesoderm and to the loss of BMP expression on the dorsal side and high expression on the ventral side of the embryo.

Indeed, luciferase reporter assays showed that non-degradable Xom is ∼20 times better at inhibiting transcriptional activation of goosecoid than wild-type Xom. Consistent with this result, embryos with non-degradable Xom have truncated heads — which is typical of an enhanced ventralized phenotype. This effect is restricted to the dorsal side, not surprisingly, as Xom's effects are restricted to that part of the embryo.

On the basis of these findings, Zhu and Kirschner propose that the correct dorsoventral BMP expression pattern in the mesoderm during gastrulation in the frog depends on the specifically timed proteolysis of Xom. But how Xom is stabilized during early gastrulation and what turns on its subsequent degradation remain unknown.