Review
Modification in reverse: the SUMO proteases

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SUMOs (small ubiquitin-like modifiers) are ubiquitin-related proteins that become covalently conjugated to cellular target proteins that are involved in a variety of processes. Frequently, this modification has a key role in regulating the activities of those targets and, thus, their cellular functions. SUMO conjugation is a highly dynamic process that can be rapidly reversed by the action of members of the Ubl (ubiquitin-like protein)-specific protease (Ulp) family. The same family of enzymes is also responsible for maturation of newly synthesized SUMOs prior to their initial conjugation. Recent advances in structural, biochemical and cell biological analysis of Ulp/SENPs reveal their high degree of specificity towards SUMO paralogs, in addition to discrimination between processing, deconjugation and chain-editing reactions. The dissimilar sub-nuclear localization patterns of Ulp/SENPs and phenotypes of Ulp/SENP mutants further indicate that different Ulp/SENPs have distinct and non-redundant roles.

Introduction

SUMO (small ubiquitin-like modifier) modulates many processes such as nuclear transport, transcription replication, recombination and chromosome segregation [1]. Like ubiquitin, SUMOs are synthesized as propeptides that require cleavage to reveal C-terminal di-glycine motifs prior to conjugation (Figure 1). Conjugation results in formation of an isopeptide bond between the SUMO C terminus and an ɛ-amino group of a lysine within the target protein. Enzymes responsible for SUMO processing and deconjugation are called Ubl (ubiquitin-like protein)-specific proteases (Ulp) in yeast [2] and Sentrin-specific proteases (SENP) in mammals [3]. Ulp/SENPs directly regulate the pools of free, conjugatable SUMO protein and the half-life of conjugated species.

Budding yeast has two Ulp/SENPs, humans have six and Arabidopsis has seven 4, 5 (Box 1). Although it is possible that novel Ulp/SENPs remain to be discovered, particularly in metazoans, the modest number of Ulp/SENPs seems striking by comparison to the number of enzymes in the ubiquitin pathway: there are >100 deubiquitylating enzymes (DUBs) in higher eukaryotes [6] but only one ubiquitin polypeptide to process or deconjugate [7]. As an understanding of the biochemical properties of Ulp/SENPs emerges, it has become clear that their enzymatic mechanisms and the determinants of their specificity show many distinct features, which will be the major topic of this review.

Section snippets

SUMO paralogs and pathway fundamentals

Budding yeast express one SUMO protein (Smt3p), whereas mammalian cells usually express three SUMO paralogs (SUMO-1, SUMO-2 and SUMO-3) [1]. Mature SUMO-1 is ∼45% identical to SUMO-2 and SUMO-3, whereas SUMO-2 and SUMO-3 are ∼95% identical to each other. The tails cleaved from each paralog are distinct. SUMO-2 and SUMO-3 have sometimes been used interchangeably in the literature. Here, we will refer to the isoform having two amino acids (Val-Tyr) after the di-glycine motif as SUMO-2 and that

Identification of Ulp/SENPs

Li and Hochstrasser [2] used an elegant sib-selection strategy to isolate SUMO proteases: they assayed cleavage of a model Smt3p substrate within extracts made from pools of bacterial transformants expressing multiple yeast proteins. Pools with cleavage activity were subdivided to isolate individual cDNAs encoding Smt3p proteases. Using this approach, they found a previously uncharacterized 72-kDa protein, which they named Ulp1p. Sequence analysis showed that Ulp1p bears no substantial

Evolutionary relations and structure of Ulp/SENPs

The C48 catalytic domain is typically located close to the C terminus of Ulp/SENPs, whereas N-terminal domains frequently direct their subcellular localization 34, 35 (Table 1). There are two major variations on this theme: in the case of Ulp2 [34] and two plant Ulp2-like proteins (NP_195088 and NP_172444. [5]), the C48 domain is in the middle of the protein instead of being C-terminal; more dramatically, the C48 domain is split in half by 50–200 amino acid insertions in vertebrate SENP6 and

Processing

The catalytic domains of SENP1 and SENP2 discriminate between SUMO paralogs as processing substrates: SENP1 processes SUMO-1 with greater efficiency than SUMO-2, but shows limited activity towards SUMO-3 44, 45. SENP2 processes SUMO-2 more efficiently than SUMO-1, but again processes SUMO-3 poorly [43]. Because Ulp/SENPs directly recognize the newly translated SUMOs in these reactions, determinants of this specificity must lie within the SUMO sequences themselves. Swapping residues that are

Regulation through sub-nuclear localization and expression patterns

The requirements for localization are best understood for Ulp/SENPs associated with the NPC. Neither enzymatic function nor rescue of Δulp1 cells requires NPC localization of Ulp1p, but this localization seems to control Ulp1p specificity [34]. Truncated Ulp1p mutants that do not bind the NPC robustly suppress growth defects of Δulp2 cells, and eliminate the majority of the Smt3p-conjugated species that characterize the Δulp2 strain. These changes have been interpreted as evidence that such

Concluding remarks

Ulp/SENPs strongly differentiate amongst processing and deconjugation substrates, arguing that they are not highly promiscuous enzymes, as was once thought. Their distinct subcellular localizations, expression patterns and genetics further argue that they have well-defined and non-redundant roles in vivo. For vertebrate cells, the capacity of Ulp/SENPs to discriminate among substrates might be particularly important for maintaining paralog-specific patterns of conjugation to cellular targets.

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