Ubiquitin-Dependent Regulation of Stem Cell Biology

Abstract

The growth of a metazoan body relies on a series of highly coordinated cell-fate decisions by stem cells which can undergo self-renewal, reversibly enter a quiescent state, or terminally commit to a cell specification program. To guide their decisions, stem cells make frequent use of ubiquitylation, a post-translational modification that can affect the activity, interaction landscape, or stability of stem cell proteins. In this review we discuss novel findings that have provided insight into ubiquitin-dependent mechanisms of stem cell control and revealed how an essential and highly conserved protein modification can shape metazoan development.

Keywords: E3 ligase; development; differentiation; stem cell; ubiquitin.

Figure 1. Hallmarks of ubiquitin-dependent signaling

A. E3 ligases determine the specificity of ubiquitin transfer by recruiting target proteins as well as an activated form of ubiquitin (~ indicates a thioester bond between ubiquitin and an active site cysteine in an E2 or E3; - denotes an isopeptide bond). E3 ligases either possess a RING-domain (RING: really interesting new gene) to recruit an E2; a HECT-domain (HECT: homologous to E6-AP C-terminus) charged with ubiquitin prior to transfer; or an RBR arrangement (RING-in between RING-RING) that also contains an active site cysteine residue. B. Ubiquitin modifications differ in their topology and function. Examples for distinct ubiquitin chain types are shown, including their major function.

Figure 2. Ubiquitylation controls stem cell quiescence, self-renewal, and differentiation

Examples of E3 ligases discussed in this review are shown on the right.

Figure 3. Ubiquitin-dependent control of Wnt signaling

A. Constitutive degradation of the β-catenin transcription factor following its phosphorylation by the destruction complex and ubiquitylation by the SCF^βTrCP E3 ligase (SCF: Skp1-CUL1-Fbox; upper case denotes specific substrate adaptor βTrCP). The destruction complex is composed of the scaffolding proteins axin and APC, the tumor suppressor Wtx1, and the kinases CK1 and GSK3β. Wnt signals prevent the destruction complex from phosphorylating β-catenin, thereby allowing β-catenin to accumulate and drive a transcriptional program supporting stem cell self-renewal. B. Ubiquitin-dependent control of Wnt receptor abundance. The E3 ligases ZNRF3 and RNF43 use the Dishevelled protein (Dvl) as an adaptor to bind and ubiquitylate the Wnt receptor Frizzled, leading to its internalization by endocytosis and to its lysosomal degradation. Secreted R-spondin proteins and their membrane receptors Lgr4/5 sequester Frizzled proteins away from ZNFR3 and RNF43, thus amplifying the Wnt signals that ensure stem cell self-renewal.

Figure 4. Regulation of stem cell fate and function by CUL3-dependent monoubiquitylation

A. CUL3^KBTBD8 controls neural crest specification by catalyzing the monoubiquityation of TCOF1 and NOLC1. This modification allows TCOF1 and NOLC1 to organize a ribosome biogenesis platform that includes RNA polymerase I (Pol-I), the H/ACA complex catalyzing pseudouridilyation (depicted as Ψ), and the SSU processome (CH₃; P for its methylation and phosphorylation activities). This ubiquitin-dependent platform leads to the production of modified ribosomes that translate specific mRNAs to drive neural crest specification. B. CUL3^KLHL12 controls COPII vesicle size and collagen secretion, a reaction critical for formation of a stem cell niche and bone. CUL3^KLHL12 catalyzes the monoubiquitylation of the COPII coat protein SEC31, thereby allowing this protein to support the formation of large COPII vesicles that accelerate the process of collagen secretion. C. To perform its cellular functions, CUL3^KLHL12 depends on a calcium-dependent co-adaptor specific for the substrate SEC31. The ALG2 subunit is only able to engage SEC31 after calcium has been released from the endoplasmic reticulum.