Wnt signals bind to Frizzled receptors to trigger canonical and noncanonical signaling responses that control cell fates during animal development and tissue homeostasis. All Wnt signals are relayed by the hub protein Dishevelled. During canonical (β-catenin–dependent) signaling, Dishevelled assembles signalosomes via dynamic head-to-tail polymerization of its Dishevelled and Axin (DIX) domain, which are cross-linked by its Dishevelled, Egl-10, and Pleckstrin (DEP) domain through a conformational switch from monomer to domain-swapped dimer. The domain-swapped conformation of DEP masks the site through which Dishevelled binds to Frizzled, implying that DEP domain swapping results in the detachment of Dishevelled from Frizzled. This would be incompatible with noncanonical Wnt signaling, which relies on long-term association between Dishevelled and Frizzled. It is therefore likely that DEP domain swapping is differentially regulated during canonical and noncanonical Wnt signaling. Here, we use NMR spectroscopy and cell-based assays to uncover intermolecular contacts in the DEP dimer that are essential for its stability and for Dishevelled function in relaying canonical Wnt signals. These contacts are mediated by an intrinsically structured sequence spanning a conserved phosphorylation site upstream of the DEP domain that serves to clamp down the swapped N-terminal α-helix onto the structural core of a reciprocal DEP molecule in the domain-swapped configuration. Mutations of this phosphorylation site and its cognate surface on the reciprocal DEP core attenuate DEP-dependent dimerization of Dishevelled and its canonical signaling activity in cells without impeding its binding to Frizzled. We propose that phosphorylation of this crucial residue could be employed to switch off canonical Wnt signaling.Wnt signaling cascades are ancient cell communication pathways that regulate cell fates during embryonic development and tissue homeostasis (
1,
2). Extracellular Wnt ligands bind to seven-pass transmembrane Frizzled receptors and transduce signals to downstream effectors through Dishevelled, an intracellular hub protein that binds to Frizzled and assembles dynamic signaling complexes termed “signalosomes” (
1,
3). Dishevelled pivots between alternative Wnt signaling branches to specify distinct outcomes (
4). These branches are broadly defined as canonical (or β-catenin–dependent), typically driving cellular proliferation or differentiation (
5,
6), and noncanonical, comprising a collection of signaling branches that coordinate cellular properties such as planar cell polarity (PCP) (
7) and morphogenetic processes such as convergent extension (
8,
9).Dishevelled has three well-conserved domains: an N-terminal Dishevelled and Axin (DIX) domain; central Postsynaptic density protein-95, Disk large tumor suppressor, Zonula occludens-1 (PDZ) domain; and C-terminal Dishevelled, Egl-10, and Pleckstrin (DEP) domain. Dishevelled is recruited to Frizzled by the DEP domain and assembles Wnt signalosomes via self-association of both its DIX and DEP domains (). The DIX domain undergoes reversible head-to-tail polymerization (
10) to generate dynamic filaments of Dishevelled that are stably cross-linked by dimerization through the DEP domain (
11). This rapidly increases the local concentration of Dishevelled and boosts its avidity for low-affinity effectors such as Axin, enabling Dishevelled to interact with these effectors even if present at a low cellular concentration (
1,
3,
12).
Open in a separate windowCartoon of DVL domain architecture and function in canonical Wnt signaling. (
A) Dishevelled with its three well-conserved domains, DIX, PDZ, and DEP. The DEP domain binds Frizzled directly through its prominent “DEP finger,” formed from the hinge loop separating H1 and H2 in the monomeric configuration. (
B) Wnt signals cause DEP to dimerize by domain swapping. During this process, H1 from one DEP molecule is exchanged with H1 from another through extension of the hinge loop. As a consequence, the “DEP finger” undergoes a conformational change, resulting in a structurally distinct β-sheet connecting the two DEP molecules, which cannot bind to Frizzed. Domain swapping therefore promotes detaching of Dishevelled from the receptor complex.The DEP domain is a small globular domain composed of three α-helices and a flexible hinge loop between the first (H1) and second helix (H2), which, in the monomeric configuration, folds back on itself to form a prominent “DEP finger” that is responsible for binding to Frizzled () (
13). DEP dimerization involves a highly unusual mechanism called “domain swapping” (
14). During this process, H1 of one DEP monomer is exchanged with H1 from a reciprocal one through outward motions of the hinge loops, replacing intra- with intermolecular contacts. This results in a dimer whose DEP cores, almost identical in structure to the monomer, are connected by a β-sheet formed between the two hinge loops () (
11). In other words, these hinge loops, which form the “DEP finger” in the monomer, undergo a major conformational change engaging in new intermolecular interactions that are likely to stabilize the dimeric configuration. Functional assays in Dishevelled null-mutant cells based on structure-designed mutants have revealed that this mechanism is essential for Wnt/β-catenin signaling (
15). There are several examples of domain swapping underlying pathological processes (e.g., in neurodegenerative disease); however, the DEP domain of Dishevelled represents a rare example of a domain undergoing physiologically relevant domain swapping (
16).
Open in a separate windowMutations attenuating DEP dimerization and DVL2-dependent signaling. (
A) Structure of the DEP dimer showing domain swapping (molecule A, dark turquoise; molecule B, light turquoise) superimposed on the DEP monomer (gray, “DEP finger”). S418 and S435 are shown (balls). (
B) SuperTOP assays of HEK293T cells, expressing wt or mutant FLAG-DVL2 (as indicated; above, corresponding Western blot); ev, empty vector control; error bars, SEM of >3 independent experiments. (
C) Western blots of immunoprecipitants (IPs) of polymerization-deficient DVL2 (M2M4-GFP) after coexpression with wt or DEP-mutant FLAG-DVL2 in transiently transfected HEK293T cells, probed with antibodies as indicated on the right; M2M4 was used instead of wt DVL2 to guard against confounding effects of DIX-dependent polymerization on DEP-dependent coIP (
11). (
D) Quantitative analysis of SNAP-FZD5-dependent recruitment of wt or mutant DEP-GFP to the plasma membrane (
n = 100 cells scored in each case). (
E) SuperTOP assays of HEK293T cells, monitoring the blocking of endogenous signaling in response to Wnt3a stimulation by overexpressed wt or mutant DEP-GFP (as indicated; above, corresponding Western blot); ev, GFP control; WCM, Wnt3a-conditioned medium (applied 6 h before lysis); error bars, SEM of >3 independent experiments. ****
P < 0.0001; one-way ANOVA with repeated measures.A consequence of domain swapping is that the Frizzled binding “DEP finger” undergoes a conformational change that is structurally incompatible with Frizzled binding () (
13). Therefore, domain swapping blocks binding between DEP and Frizzled, which could cause detachment of Dishevelled from Frizzled. In turn, this would terminate Wnt signal transduction, as the signal relay depends on continued association between Frizzled and Dishevelled. For example, PCP signaling in
Drosophila requires apical recruitment of Dishevelled (Dsh) by Frizzled to be maintained for many hours, even days, in stable, membrane-localized signalosomes that are clearly visible by confocal microscopy (
17,
18). In contrast, Wnt/β-catenin signaling appears to need only a transient association between Frizzled and Dsh. This is illustrated by
dsh1 flies that bear a mutation in the DEP finger (K417M), which reduces the membrane localization of Dishevelled and thus causes PCP defects without apparently affecting canonical Wnt signaling (
7,
19,
20). The same mutation in Dvl2 (K446M) causes PCP and convergent extension defects when introduced into
Dvl1−/− Dvl2−/− transgenic mice (
21). Thus, either DEP domain swapping needs to be attenuated in PCP signalosomes or, if domain-swapped Dishevelled molecules were to remain within signalosomes, adaptor proteins would be required to mediate continued association between Dishevelled and Frizzled receptor complexes.One mechanism by which the DEP domain could be regulated is by Wnt-induced phosphorylation (
19,
20,
22), which accompanies the “activation” of Dishevelled (
23,
24). During PCP signaling in flies, phosphorylation of Dishevelled correlates with its membrane recruitment by Frizzled (
19,
20). Furthermore, its phosphorylation by Discs Overgrown (Dco), the
Drosophila casein kinase-1ε (CK1ε) ortholog, promotes asymmetric localization of Dishevelled along the apical plasma membrane (
25) and its stable association with junctional complexes (
26). Dishevelled is phosphorylated on numerous serine (Ser) and threonine (Thr) residues, but it is unclear which of these are biologically important, as the vast majority of phosphorylations detected by mass spectrometry (MS) are not required for function or are functionally redundant (
22,
25,
27,
28). However, we previously reported that single point mutations of two conserved Ser residues in the DEP domain (S418 and S435) reduce Wnt/β-catenin signaling (
11) (
SI Appendix, Fig. S1), suggesting that the phosphorylation of either Ser could regulate DEP domain function. Importantly, S418 is clearly a substrate for phosphorylation since high-throughput analysis of phosphorylation sites in breast cancer samples detected S418 phosphorylation by MS (
29) (PhosphoSite). In addition, a recent comparative analysis of human Dishevelled-3 (DVL3) phosphorylation revealed that several Ser/Thr kinases are capable of phosphorylating S407 (the equivalent of DVL2 S418) in cells (
30). Whether S435 is a bona fide substrate for phosphorylation remains to be determined; however, phosphorylation of its equivalent in flies, S406, was detected by MS in cells undergoing PCP signaling (
28). Based on this evidence, we decided to investigate whether these or any other phospho-sites in the DEP domain affect signaling by altering DEP domain swapping.Here, we show that these two highly conserved Ser residues (S418 and S435) are required for the stability of the DVL2 domain-swapped DEP dimer. We used NMR spectroscopy to demonstrate that S418, located immediately upstream of H1, engages in crucial noncovalent interactions with a structured loop that connects H2 and H3. As a consequence, a β-sheet forms that clamps down each H1 onto its reciprocal DEP core within a domain-swapped dimer, thereby providing stability to this DEP dimer without, however, affecting the binding between DEP monomer and Frizzled. An important corollary is that the phosphorylation of the key residue S418 within this clamp, for example, during noncanonical Wnt signaling, attenuates domain swapping, thereby allowing a stable association between DEP monomers and Frizzled. Our work has uncovered a pivotal residue within Dishevelled that negatively regulates DEP domain swapping, thereby antagonizing canonical Wnt signaling.
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