Commentary 539Introduction Ubiquitylation [also known as ubiquitination, as coined by the discoverers of this modification with regard to its connection to proteolysis (Wilkinson, 2005)] is a three-step enzymatic reaction that is carried out by several enzymes: the ubiquitin-activating enzyme (E1), a ubiquitin carrier protein (E2; also known as ubiquitin-conjugating enzyme, UBC) and a ubiquitin-protein ligase (E3). An additional component of the ubiquitylation machinery has been described. This E4 enzyme is involved in elongation of short ubiquitin chains (Koegl et al., 1999). However, the requirement for an E4 activity appears to be limited to a small subset of substrates. Ubiquitylation-dependent proteasomal degradation is involved in the regulation of numerous cellular processes, including cell cycle progression, apoptosis, DNA repair, the maintenance of cellular quality control, autophagy, the regulation of transcription and receptor-mediated endocytosis (Mayer et al., 2005;Mayer et al., 2006;Mayer et al., 2008). In general, modification by ubiquitin serves as a recognition element in trans, whereby different downstream effectors bind to the ubiquitin-modified protein to affect its fate and/or function. In the case of proteasomal degradation, the ubiquitylated protein is recognized by the 26S proteasome and subsequently degraded (Dikic et al., 2009;Su and Lau, 2009).The widely accepted canonical signal for proteasomal degradation is a polyubiquitin chain that is anchored to the -NH 2 group of a lysine residue(s) in the substrate by an isopeptide bond and is assembled through the formation of isopeptide bonds between the C-terminal residue of one ubiquitin moiety (glycine 76) and lysine 48 of the previously conjugated ubiquitin moiety (Chau et al., 1989). Recent studies have reported, however, that other types of ubiquitin chains can also be recognized by the proteasome (Figs 1, 2). These include an ester-based linkage that connects ubiquitin to a threonine or serine residue in the substrate, and a thiolester-based linkage whereby ubiquitin is bound to a cysteine residue in the substrate (McDowell et al., 2010;Tait et al., 2007;Vosper et al., 2009). Ubiquitin can also be conjugated to the -NH 2 group of the N-terminal residue of the substrate. Instead of using lysine 48 for the linkage, polyubiquitin chains can also be assembled through one of the six additional lysine residues in the molecule. Such homogenous chains based on, for example, lysine 63 (Saeki et al., 2009), or heterogeneous chains in which different ubiquitinubiquitin linkages are found, have also been reported to target proteins for proteasomal degradation. Linear chains, in which the ubiquitin links are attached to one another 'head-to-tail', and heterologous chains, in which the links are made of ubiquitin and a ubiquitin-like protein, such as small ubiquitin-like modifier (SUMO), have additionally been shown to target proteins for proteasomal degradation. Surprisingly, it has been demonstrated that the proteasome does not necessarily have ...