A SIM-ultaneous role for SUMO and ubiquitin J. Jefferson P. Perry 1, 2 , John A. Tainer 1, 3 and Michael N. Boddy 1 1 Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA 2 The School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappanna (P.O.) Kollam, Kerala, India 3 Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Ubiquitin and ubiquitin-like proteins (Ubls) share a b-GRASP fold and have key roles in cellular growth and suppression of genome instability. Despite their common fold, SUMO and ubiquitin are classically por- trayed as distinct, and they can have antagonistic roles. Recently, a new family of proteins, the small ubiquitin- related modifier (SUMO)-targeted ubiquitin ligases (STUbLs), which directly connect sumoylation and ubi- quitylation, has been discovered. Uniquely, STUbLs use SUMO-interaction motifs (SIMs) to recognize their sumoylated targets. STUbLs are global regulators of protein sumoylation levels, and cells lacking STUbLs display genomic instability and hypersensitivity to gen- otoxic stress. The human STUbL, RNF4, is implicated in several diseases including cancer, highlighting the importance of characterizing the cellular functions of STUbLs. Ubiquitin-like domains Covalent post-translational modifications regulate protein function and are collectively required for cell viability. Ubiquitin and ubiquitin-like proteins (Ubls; see Glossary), including SUMO (small ubiquitin-like modifier), are a subset of these modifications [1]. Despite their lack of sequence similarity, ubiquitin and SUMO are small, single-domain proteins that share the same b-GRASP fold [2,3]. However, their surface residues and charge distri- butions are significantly different, supporting the distinct functions of SUMO and ubiquitin mediated by separate sets of enzyme and substrate partners. A further difference includes the existence of three major SUMO isoforms (SUMO1–3) versus a single form of ubiquitin. SUMO2 and SUMO3 are almost identical and are able to form chains owing to a flexible N terminus, which is absent in the more divergent SUMO1. All these differences between ubiquitin and the SUMO isoforms translate into distinct physiological roles. Initially, ubiquitin was identified for its ability to target proteins for degradation by the 26S pro- teasome, whereas SUMO was characterized for performing an opposing role, stabilizing target proteins. Thus, classi- cally, the SUMO and ubiquitin pathways have been described as having a largely antagonistic relationship [4,5]. However, further studies have revealed that SUMO and ubiquitin are not simply antagonistic but display more subtle modes of interplay (for further reading on this interplay, see Ref. [6]). There are also complex relationships between Ubl modifiers and other post-trans- lational modifications, including acetylation and phos- phorylation [7]. This interplay provides for a wide field of functions, including roles in DNA repair, cell-cycle con- trol, stress responses, signaling, endocytosis and vesicular trafficking [6,8]. The covalent attachment of ubiquitin and Ubls requires sequential steps executed by E1, E2 and E3 enzymes that catalyze bond formation between ubiquitin or the Ubl C- terminal glycine and a lysine residue in the target protein [8] (Figure 1). Notably, multiple rounds of this modification process lead to the formation of SUMO or ubiquitin chains. These chains can elicit a different cellular response to those elicited by the single modifications. For example, ubiquitin chains formed on Lys48 result in proteasomal targeting, whereas Lys63 chains have non-proteasomal roles, including functions in DNA repair [4]. SUMO2 and SUMO3 chains were first observed in mammalian cells, and both isoforms can form chains in vitro [9]. In Saccharomyces cerevisiae (budding yeast), SUMO (Smt3p) chains, which are not required for viability but might have a regulatory role in meiotic progression, accumulate to toxic levels in cells lacking the desumoylating enzyme Ulp2p [10,11]. Review Corresponding authors: Tainer, J.A. (jat@scripps.edu); Boddy, M.N. (nboddy@scripps.edu). Glossary E1, E2 and E3 enzymes: an E1-activating enzyme (with ATP) adenylates the C- terminal carboxyl group of ubiquitin or Ubl, which forms a high-energy ubiquitin–AMP or Ubl–AMP intermediate. This intermediate is then attacked by the E1 active-site cysteine, forming an E1-ubiquitin or E1-Ubl thioester. The activated ubiquitin or Ubl is transferred to the active-site cysteine of the E2- conjugating enzyme. The ubiquitin or Ubl moiety is then ligated to an acceptor lysine in a target protein in a process stimulated by an E3 ligase, for example, the RING finger protein. b-GRASP fold: this fold is built from a domain in which the b-sheet seems to ’grasp’ its helical segment, and hence was named b-GRASP. This fold was first recognized in ubiquitin- and immunoglobulin-binding domains of Gram- positive bacteria and is now observed in other polypeptides, including the ubiquitin-like proteins. SUMO-interaction motifs (SIMs): mediate the non-covalent interactions of SIM-containing proteins with SUMO. SIMs are typically short hydrophobic peptide sequences that, in some cases, are preceded, or followed, by a stretch of acidic amino acids. SUMO-targeted ubiquitin ligases (STUbLs): a new class of ubiquitin ligases that are targeted to, and ubiquitylate, sumoylated proteins. Ubiquitin-like proteins (Ubls): a family of proteins that includes SUMO, ISG15 (interferon-stimulated gene 15) and Nedd8 (neural precursor cell expressed developmentally downregulated 8), which are covalently attached to target proteins to modify their functions by promoting new interactions, altered localization or degradation. ULPs (Ubl-specific proteases): enzymes required for both the C-terminal processing ‘maturation’ of SUMO and its removal from target proteins. TIBS-564; No of Pages 8 0968-0004/$ – see front matter . Published by Elsevier Ltd. doi:10.1016/j.tibs.2008.02.001 Available online xxxxxx 1