The ubiquitination code: a signalling problem

Abstract

Ubiquitin is a highly versatile post-translational modification that controls virtually all types of cellular events. Over the past ten years we have learned that diverse forms of ubiquitin modifications and of ubiquitin binding modules co-exist in the cell, giving rise to complex networks of protein:protein interactions. A central problem that continues to puzzle ubiquitinologists is how cells translate this myriad of stimuli into highly specific responses. This is a classical signalling problem. Here, we draw parallels with the phosphorylation signalling pathway and we discuss the expanding repertoire of ubiquitin signals, signal tranducers and signalling-regulated E3 enzymes. We examine recent advances in the field, including a new mechanism of regulation of E3 ligases that relies on ubiquitination.

Figure 1

The ubiquitin pathway. A) Schematic representation of the ubiquitination process. A hierarchical set of three types of enzyme is required for substrate ubiquitination: ubiquitin-activating (E1), ubiquitin-conjugating (E2) and ubiquitin-protein ligase (E3) enzymes. The two major classes of E3 ligases are depicted. B) Schematic representation of the different Ub modifications with their functional roles. The question mark indicates that the functions of branched chains are largely unknown.

Figure 2

Dose-dependent entry routes for the EGFR. A) At low doses of EGF, EGFR is mainly internalized through clathrin pathway (CME, clathrin-mediated endocytosis). In this condition, ubiquitination of the receptor is not required for its internalization. B) At higher doses of EGF, CME is equally active but a significant part of EGFR internalization proceeds also to an alternative pathway (NCE, non-clathrin endocytosis). The exact nature, and the molecular determinants, of this "alternative" pathway are still controversial. Essentially NCE is defined by its insensitivity to functional ablation (KD) of clathrin and sensitivity to cholesterol-interfering drugs, like filipin. Hence, its definition as a "raft-dependent pathway". Internalization of EGFR through NCE requires receptor ubiquitination. Multiple roles of Eps15/R and epsin in the different internalization pathways are also shown (see main text for detailed explanations).

Figure 3

"Hand-off" mechanism model for ubiquitinated cargos. Ub receptors (A and C), recognizing the hydrophobic patch centred on Ile44 (depicted in black), are intercalated with others (B), recognizing different region of Ub (depicted in white). Rabex-5, through ZnF_A20 domain, recognizes the polar patch centred on Asp58 and represents an example of Ub receptors B. Endosome is depicted as prototype of trafficking organelles.

Figure 4

Regulation of E3 activities by post-translational modifications. A) Extracellular stimuli can induce various post-translational modifications of E3 ligases. This might result on a positive or a negative regulation of the ligase activity. Examples are reported (see main text for detailed explanations). The arrows represent the integration of numerous signals. pY, tyrosine phosphorylation; pS/T, serine or threonine phosphorylation; Ub, ubiquitination; Ub-like, neddylation or sumoylation. B) Comparison between the phospho-based network and the Ub-based network. Similarity includes recognition by dedicated protein domains (SH2 and UIM are example), inducibility by upstream signals and reversibility (DUBs work as phosphatases). In addition, kinases are often activated by tyrosine phosphorylation in the signalling cascade while E3 ligases could be activated by ubiquitination.