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SUMO-Specific Proteases/Isopeptidases: Senps and Beyond Arnab Nayak and Stefan Müller*

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SUMO-Specific Proteases/Isopeptidases: Senps and Beyond Arnab Nayak and Stefan Müller* Nayak and Müller Genome Biology 2014, 15:422 http://genomebiology.com/2014/15/1/422 PROTEIN FAMILY REVIEW SUMO-specific proteases/isopeptidases: SENPs and beyond Arnab Nayak and Stefan Müller* cascade. Modification by SUMO generally controls Abstract protein-protein interactions by recruiting binding part- We summarize the evolutionary relationship, structure ners that harbor specific SUMO-interaction motifs and subcellular distribution of SUMO proteases (SIMs). (or SUMO isopeptidases). We also discuss their functions Regulated deconjugation of SUMO from its substrates is and allude to their involvement in human disease. a central element of the SUMO system as it assures the plasticity of protein interaction networks. The deconjuga- Keywords: SUMO, SUMO isopeptidase, SUMO-specific tion process is catalyzed by a family of cysteine proteases, protease, SENP, Desi-1, Desi-2, USPL1 termed SUMO isopeptidases or SUMO-specific proteases. Members of this enzyme class function as deconjugating Introduction enzymes for isopeptide-linked SUMO-protein conjugates The ubiquitin-like SUMO (small ubiquitin-related modi- and also depolymerize isopeptide-linked poly-SUMO2/3 fier) system is a post-translational protein modification chains. Moreover, some family members act as processing pathway in eukaryotes [1,2]. SUMOylation is a highly dy- factors for the carboxy-terminal maturation of the SUMO namic process, where deconjugation (deSUMOylation) is precursor. The known SUMO-specific isopeptidases and catalyzed by a family of cysteine proteases, termed proteases are cysteine proteases that are classified into SUMO-specific proteases or SUMO isopeptidases. A three distinct families: the Ulp/SENP (ubiquitin-like prote- subset of these enzymes also functions in processing of ase/sentrin-specific protease) family, the Desi (deSUMOy- the SUMO precursor proteins, which is a prerequisite lating isopeptidase) family and USPL1 (ubiquitin-specific for their conjugation. In this review, we summarize the peptidase-like protein 1). current view of SUMO deconjugating enzymes. We dis- cuss their evolutionary relationships, subcellular distri- Gene organization and evolutionary history butions and functions as well as their involvement in All identified SUMO isopeptidases/proteases are cyst- human disease. eine proteases. They share a similar catalytic mechanism SUMO belongs to the family of ubiquitin-like proteins. but belong to different superfamilies that are distin- Like ubiquitin, it functions as a protein modifier that is guished by the fold of their respective catalytic domains. ε covalently attached to -amino groups of lysine residues Ulp/SENP proteins belong to the C48 family subgroup of target proteins [1,2]. Lower eukaryotes attach a single of the CE superfamily of thiol proteases whose founder SUMO form (known as smt3) to target proteins, member is Ulp1, first discovered in the yeast Saccharo- whereas the human SUMO system makes use of three myces cerevisiae [3]. Subsequently, Ulp2 was identified related SUMO forms (SUMO1, SUMO2 and SUMO3). as a second SUMO-deconjugating enzyme in yeast [4]. All SUMO/smt3 forms are expressed as precursor pro- Ulp1/2-related isopeptidase genes are also found in the teins that require carboxy-terminal proteolytic process- genome of Drosophila melanogaster [5,6]. In higher eu- ing prior to their conjugation. Processing exposes a karyotes, the family is more diverse. Seven human pro- carboxy-terminal di-glycine motif, which is essential for teins were initially classified as Ulp family members and conjugation. Subsequent conjugation proceeds by a annotated as SENPs [7]. (The term sentrin was coined pathway that typically involves an E1-E2-E3 enzymatic by Ed Yeh as an alternative name for SUMOs.) Notably, however, later experimental work revealed that SENP8 * Correspondence: [email protected] acts on the ubiquitin-family member Nedd8, but not on Institute of Biochemistry II, Goethe University, Faculty of Medicine, SUMO paralogs [8,9]. The human genome therefore Theodor-Stern-Kai 7, 60590 Frankfurt, Germany © 2014 Nayak and Muller; licensee BioMed Central Ltd. The licensee has exclusive rights to distribute this article, in any medium, for 12 months following its publication. After this time, the article is available under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Nayak and Müller Genome Biology 2014, 15:422 Page 2 of 7 http://genomebiology.com/2014/15/1/422 encodes six dedicated SUMO-specific members of the SUMO protease Length Ulp/SENP family: SENP1, SENP2, SENP3, SENP5, SENP6 and SENP7. Sequence analyses and phylogenetic Ulp1 621 comparison of the human SENPs with Ulp1 and Ulp2 Ulp2 1034 from lower eukaryotes illustrate that SENP1, SENP2, SENP1 644 SENP3 and SENP5 are evolutionarily related to the Ulp1 100% branch, whereas SENP6 and SENP7 are related to the SENP2 589 Ulp2 branch (Figure 1). The tree further reveals the pair- 60% SENP3 574 wise similarity of SENP1 to SENP2, SENP3 to SENP5 44% and SENP6 to SENP7. SENP5 755 The deSUMOylating isopeptidases Desi-1 and Desi-2 46% SENP6 1112 belong to the evolutionarily distinct C97 family of cyst- 32% eine proteases [10]. Orthologs of Desi-1 and Desi-2 are SENP7 984 21% found in plants and metazoa, but are missing in lower eukaryotes such as yeast. DESI1 168 DESI2 USPL1 is, to date, the only known mammalian 194 SUMO-specific protease of the C98 family [11]. USPL1- USPL1 1092 related deconjugases are found in metazoan vertebrates Figure 2 Structural organization of SUMO-specific-proteases/ and invertebrates. USPL1 is not related to the Ulp/SENP isopeptidases. The domain organizations of Ulp/SENPs and Desi and Desi families, but the catalytic domain of USPL1 family members are shown. Green ovals represent the catalytic shows homology to the C19 family of ubiquitin-specific domain. The sequence determinants that are responsible for proteases. For example, within this region, USPL1 shares subcellular targeting are represented by orange ovals. The length of the proteins as total number of amino acids is presented on the around 20% sequence identity with the ubiquitin- right side. For the catalytic domains of SENP family members, deconjugating enzyme USP1. sequence identity shared with SENP1 is also shown. Characteristic structural features SENP2, SENP3-SENP5 and SENP6-SENP7 pairs show The common characteristic of the Ulp/SENP family is the highest degree of similarity to each other. SENP6 their conserved catalytic domain, which spans around and SENP7 are most divergent from the rest of the 200 amino acids in the carboxy-terminal part of the pro- family and harbor conserved sequence insertions within tein (Figure 2). This domain has sequence and structural their catalytic domains. Structural data describing the similarity to the catalytic region of adenoviral proteases, catalytic domain of yeast Ulp1 and human SENP1 and which cleave viral and cellular proteins. The human SENP2 in complex with SUMO precursors or Ulp/SENP family members share 20 to 60% sequence isopeptide-linked SUMO-RanGAP1 conjugates revealed identity within their catalytic domains. The SENP1- important insights into the catalytic features of this en- zyme class [12-16]. The active site cysteine residue is embedded in a typical catalytic triad (Cys-His-Asp). An 0.94 Dm_ULP2 additional invariant Gln residue in close proximity stabi- human_SENP7 0.83 0.97 human_SENP6 lizes the transition state during catalysis. The substrate S.c._ULP2 accesses the catalytic site through a shallow tunnel, in S.c._ULP2 which conserved Trp residues are essential for position- 0.83 0.69 human_SENP2 0.84 human_SENP1 ing the di-glycine motif and the scissile bond over the 0.38 Dm_Ulp1 active site. A remarkable finding was that the scissile 1 human_SENP5 human_SENP3 bond of the pre-SUMO variants or a SUMO-conjugate Figure 1 Evolutionary relationship of Ulp/SENP family is oriented in a cis configuration for cleavage [14,15]. members. The phylogenetic tree displays the relationship between In addition to their conserved catalytic domain, all Saccharomyces cerevisiae (S.c.), Drosophila melanogaster (Dm) and SENPs have amino-terminal regions of variable length human Ulp/SENP family members. Confidence numbers generated that have crucial regulatory functions. These regions fre- by the bootstrapping procedure are shown for each branch in the tree. The following sequences were used for input: SENP1 UniProtKB, quently contain interaction domains for cellular adaptor Q9P0U3; SENP2 UniProtKB, Q9HC62; SENP3 UniProtKB, Q9H4L4; proteins that determine the subcellular distribution of SENP5 UniProtKB, Q96HI0; SENP6 UniProtKB, Q9GZR1; SENP7 Ulp/SENP family members [17-19]. Post-translational UniProtKB, Q9BQF6; Dm_ULP1, GenBank AAF48933.1; Dm_ULP2 modifications, such as phosphorylation or ubiquitylation, (Velo; verloren), GenBank AAS65070.1; S.c._ULP1, UniProtKB/Swiss- within these regions provide additional regulatory layers Prot Q02724.1; S.c._ULP2, UniProtKB/Swiss-Prot P40537. for the recruitment of binding partners or the control of Nayak and Müller Genome Biology 2014, 15:422 Page 3 of 7 http://genomebiology.com/2014/15/1/422 Ulp/SENP stability [20-23]. Interestingly,
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