PII: S0968-0004(01)01835-7

Research Update We anticipate that further experimental investigation of the specific role of each of the five classes of Brix domain proteins in eukaryote model organisms, especially in yeast, will yield valuable new insights about ribosome synthesis and be key to our understanding of the ribosome biogenesis pathway. Acknowledgements We are grateful to E. Bogengruber, M. Breitenbach, F.M. Jantsch and G. Lepperdinger for supplying experimental data on sequence and function of Brix (AF319877) and yol077c before publication and for extensive discussion of the Brix sequence analysis results. This research was supported by Boehringer-Ingelheim International. Ubiquitin is a small protein, highly conserved among eukaryotes, that becomes covalently attached to both itself and a variety of cellular proteins 1,2 . The role of this ubiquitination is mostly to target proteins to the 26S proteasome degradation pathway 3 . In some cases, monoubiquitination (e.g. of histones) does not lead to degradation, but instead regulates other cellular processes such as chromatin remodeling 4 . Recently, several reports have described a role for monoubiquitination in a different pathway of protein degradation -the endocytosis and subsequent proteolysis of receptors and other transmembrane proteins by the vacuole or the lysosome 5,6 . According to the current model, the decisions about which protein is to be degraded at a specific time is made by the ubiquitination machinery, often in response to a prior event such as phosphorylation. Consequently, both the proteasome and the endocytosis machinery need a mechanism by which to faithfully recognize ubiquitinated proteins. The 26S proteasome comprises two main particles: the 20S core proteasome and the 19S regulatory complex. Subunit S5a (also known as Rpn10) of the 19S regulator binds polyubiquitin chains and has a preference for chains containing four or more ubiquitin monomers. The ubiquitin-interacting region has been mapped to two short, related motifs that are found in all members of the S5a family 7 . Using these regions, which comprise ~20 residues, as a starting point, we searched for other potential ubiquitin-binding sequences. Specifically, we used a combination of iterative database searches with generalized profiles, and Hidden Markov Models (profile-HMMs) 8 . Only sequences that matched a profile or an HMM derived from previously established family members, with error probabilities of p < 0.01, were used for subsequent iteration cycles. After eight cycles, the sequence motif 4 Migeon, J.C. et al. (1999) converged to a set of proteins shown in An observation of particular interest is the occurrence of UIMs in four classes of proteins involved in receptor endocytosisthe Eps15 subfamily of EH-domain proteins, the epsin subfamily of ENTH-domain proteins and two families of VHS-domain proteins, including the FYVE-finger proteins HRS and Vps27, and the SH3-domain proteins STAM and HBP. Eps15 is phosphorylated on Tyr850 by the ligandactivated epidermal growth factor (EGF) receptor and this phosphorylation is required for subsequent receptor endocytosis 10 . Furthermore, Eps15 binds to epsin, and both of these proteins interact with components of the endocytosis machinery, including clathrin and the AP-2 complex 11,12 . The fact that the phosphorylation site of Eps15 is immediately adjacent to a tandem UIM suggests that this motif might be involved in the regulated endocytosis of the EGF receptor. Liquid facets (lqf), an epsin from Drosophila melanogaster, was identified in a genetic screen as a dominant enhancer of the fat facets (faf) mutant eye phenotype 13 . This relationship links the gene encoding lqf with the ubiquitin system because faf is a deubiquitinating enzyme. An additional link between Eps15 and ubiquitin recognition is provided by the yeast protein Ede1p, the closest homolog of mammalian Eps15 (Ref. 14): in the yeast protein, the UIM is replaced by a UBA domain, a homology domain known to bind ubiquitin 15 . Proteins with an N-terminal VHS domain can be divided into three subtypes on the basis of their domain organization: (1) Vps27-HRS-like (type A); (2) STAM-HBP-like (type B); and (3) other proteins (type C) (se