A new class of SUMO proteases.

The small ubiquitin-related modifier (SUMO) is a ubiquitin-like (UBL) protein that can be conjugated to hundreds of different proteins. Such ‘sumoylation’—which is highly dynamic— alters the stability, localization or functional properties of the modified substrate, most often by altering its interactions with other proteins [1,2]. Enzymes known to remove SUMO from substrates, the SUMO proteases, have important regulatory roles, and until now all those described belong to the same protein superfamily. A study in this issue of EMBO reports provides the first unambiguous biochemical identification of a novel type of SUMO protease, which is broadly conserved and important for the regulation of a specific transcription factor [3]. These and other recent results raise the exciting prospect of additional SUMO proteases still to be discovered. SUMO is covalently attached to substrate lysine side chains through a wellknown enzymatic cascade (Fig 1A; [1]). Vertebrates encode at least three functioning SUMO proteins: SUMO1, and the nearly identical SUMO2 and SUMO3. All are synthesized with carboxy-terminal propeptides that must be removed; the mature C-terminus is then coupled by amide or ‘isopeptide’ linkage to substrate lysines. Only a small fraction of most substrates is modified by SUMO at any given time. This is often due to the high rate of enzymatic cleavage of the SUMO–protein isopeptide bond by SUMO proteases or isopeptidases. The first identified SUMO protease Ulp1 (ubiquitin-like protein-specific protease 1), was isolated in an activity-based screen of proteins from the yeast Saccharomyces cerevisiae [4]. All other known SUMO proteases have been identified by virtue of their sequence similarity to yeast Ulp1. S. cerevisiae has a second, related SUMO protease, Ulp2, whereas humans have six, known as SUMO/sentrin-specific proteases (SENPs) [5]. A seventh, more divergent human ULP/SENP enzyme, SENP8, is specific for another UBL, NEDD8. Notably, the ULP/SENP enzymes constitute a branch within a larger group of proteases, the CE clan of cysteine proteases. Similarly to SENP8, not all CE clan enzymes are SUMO proteases. For example, a bacterial protein, ElaD, is a ubiquitin-specific protease, and many clan members from viruses are primarily involved in viral polyprotein processing [6]. The answer to the converse question, whether all SUMO proteases are ULP/SENP enzymes, has been less clear. A candidate for a novel SUMO protease is Wss1 (weak suppressor of smt3-1), an S. cerevisiae protein identified originally as a high-copy suppressor of a mutant version of SMT3, the yeast SUMO gene [7]. Subsequent bioinformatic analysis predicted that Wss1 was a zinc-dependent protease, the founding member of the WLM (Wss1-like metalloprotease) family [8]. Yeast wss1 mutations show extensive genetic inter actions with other SUMO pathway mutations, including those in the SUMO proteases [9]. Biochemical experiments with engineered substrates suggested that Wss1 could cleave the linkage between SUMO and a polypeptide, but this specificity did not extend to other substrates [9]. Thus, it remains unclear whether Wss1 has a broader specificity, A new class of SUMO proteases