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Cell Science at a Glance 4249

SUMOylation and and this pathway has been implicated in SUMO-3. SUMO-2 and SUMO-3 are ~95%
controlling many aspects of cell physiology, identical to each other. In most contexts,
deSUMOylation at a including cell-cycle regulation, transcription, SUMO-2 and SUMO-3 cannot be distinguished,
glance nucleocytoplasmic transport, DNA replication and here we collectively refer to them as
and repair, chromosome dynamics, SUMO-2/3. SUMO-2 and SUMO-3 are each
Yonggang Wang and apoptosis, and ribosome biogenesis. ~45% identical to SUMO-1, and all mammalian
Mary Dasso* Both SUMOylation and deSUMOylation paralogues are ~ 45% identical to Smt3p.
Laboratory of Gene Regulation and Development, (SUMO deconjugation) are highly dynamic There are several important differences
National Institute of Child Health and Human processes. This poster article discusses the between the mammalian SUMO paralogues.
Development, Bethesda, MD 20892, USA
enzymes that mediate SUMOylation and First, some SUMO targets are conjugated only to
*Author for correspondence (mdasso@helix.nih.gov)
deSUMOylation, concentrating on their SUMO-1, others only to SUMO-2/3, and still
Journal of Cell Science 122, 4249-4252 mechanisms of action. Although it is not others to all SUMO paralogues (Vertegaal
Published by The Company of Biologists 2009
doi:10.1242/jcs.050542 possible to discuss individual SUMOylated et al., 2006). Second, the overall cellular
targets in detail, we will mention emerging concentration of SUMO-2/3 is greater than that of
paradigms that explain how SUMOylation SUMO-1, as is the pool of free protein available
Small ubiquitin-related modifiers (SUMOs) are might direct the fate of target proteins. for conjugation (Saitoh and Hinchey, 2000). It is
ubiquitin-like polypeptides that become thus likely that the bulk of SUMOylation
covalently conjugated to cellular proteins in a SUMO paralogues involves SUMO-2/3. Third, SUMO-1 and
manner similar to ubiquitylation (Johnson, Yeast express a single SUMO paralogue, called SUMO-2/3 show different subcellular
2004). More than 1000 proteins have been Smt3p in Saccharomyces cerevisiae. localization patterns (Ayaydin and Dasso, 2004;
identified as potential SUMO-conjugation Mammalian cells express three major SUMO Zhang et al., 2008). Fourth, photobleaching
(SUMOylation) targets (Hochstrasser, 2009), paralogues, called SUMO-1, SUMO-2 and experiments suggest that SUMO-1 is less
Journal of Cell Science

SUMOylation and DeSUMOylation at a Glance


jcs.biologists.org
Yonggang Wang and Mary Dasso

Key steps and components in the SUMO pathway SUMOylation confers multiple fates

S-1 a. Blocking a binding site


1. 2. 3. 4. 3.
Cleavage SUMO SUMO SUMOylation DeSUMOylation K
of SUMO activation transfer to of target (see below) Interactor
C-terminus (linkage to E2 enzyme (E3-dependent
Target Cell-cycle regulation
E1 enzyme) or -independent; SUMO-1 Interactor Gene transcription
see below) S Nucleocytoplasmic transport
E1, E2, E3 K K
SUMOylation
Target
T
Target DNA replication and repair
Ulp/SENP Target
arget
Aos1 Chromosome dynamics
SH DeSUMOylation
K
K Apoptosis
Uba2 SH Ubc9 Target S Ribosome biogenesis
Aos1 Target b. Creation of additional binding site
E3s Ulp/SENP Others
Ubc9

K K
S S Uba2 S S S S Target Target

Ulp/SENP AMP+PPi Aos1 SH Interactor


ATP Ulp/SENP Interactor
Uba2 SH Ubc9 SIM
SUMO-2/3 S-2/3 SIM S
K SUMOylation K
S E1, E2, E3
K Target Target S-2/3
Target DeSUMOylation S-2/3
T r e
S-2/3
Mammals S. cerevisiae S. pombe c. Conformation alteration g
a
Small ubiquitin-related modifiers SUMO-1, SUMO-2, SUMO-3 Smt3p Pmt3p
S S-2/3n
Activating enzyme (E1) Aos1 (Sae1)-Uba2 (Sae2) Aos1p-Uba2p Rad31p-Fub2p t
SUMO-2/3n K SUMOylation K
Ulp/SENP
Conjugating enzyme (E2) Ubc9 Ubc9p Hus5p E1, E2, E3 Target Target
SP-RING-type E3 ligases PIAS1, PIAS3, PIASxα (ARIP3), Siz1p (UII1p), Pli1p, Nse2p S-1 DeSUMOylation

PIASxβ (Miz1), PIASγ (PIAS4), Siz2p (Nfi1p),


K
Mms21 (Nse2) Mms21p
S-2/3
(Nse2p), Zip3p S-2/3
Un
IR E3 ligase RanBP2 (Nup358) K U
K U
Other E3 ligases HDAC4, KAP1, Pc2, Topors S-2/3n U Proteasome-mediated
S-2/3n
Ubiquitin degradation
Protease (Ulp/SENP) SENP1 (SuPr-2), SENP2 (SMT3IP2, UIp1p (Nib1p), Ulp1p, Ulp2p
Ulp/SENP E1, E2, STUbL Un S-2/3n
K K U S-2/3
SSP3, Axam2), SENP3 (SMT3IP1), Ulp2p (Smt4p)
Target Target U S-2/3
SENP5 (SMT3IP3), SENP6 (SSP1, U S-2/3
SUMO-1
SUSP1), SENP7 DUB K K
E1, E2, E3
Target

E3-dependent (Siz/PIAS-mediated) SUMOylation E3-independent (SIM-mediated) SUMOylation Mechanism of SUMO deconjugation by Ulp/SENP
NH2
K
Siz/ S Ulp/SENP S
c9 Gly O Gly
HS
Ub Target
9

O
PIAS
Ubc

O O S-Cys
Siz/ O Cys NH
c9 c9
S

NH
G

O
9
O

SGly Ub SGly
ly

PIAS S S
Ub S
Gly O
S Gly S
Ub
c S s
K K
S

O Cys Cys
NH Cys Gly Cy O
Target Ulp/SENP S
C

c9 Siz/ Siz/ S Ubc9 Target O Gly


ys

SGly SIM NH Gly S


S
Ub PIAS PIAS
NH2 K
SIM
K
S-Cys
Cys K SIM K NH2 K NH2 Target
NH2 Target Target Substrate Enzyme-bound substrate Thioester intermediate
SIM K NH2 Target
K Target (trans conformation) (cis conformation)
Target H2O
Target c9
Ub
HS
Cys S
O Gly

Ubc9-bound Free target Siz/PIAS and Ubc9- Conjugate Free target SIM-mediated Enzyme-bound Conjugate
OH Ulp/SENP S
O Gly
Ulp/SENP
SUMO bound substrate bound intermediate substrate HS-Cys OH HS-Cys

Free enzyme Product-bound enzyme

Abbreviations: DUB, deubiquitylating enzyme; E3s, E3 ligases; HDAC4, histone deacetylase 4; IR, internal repeat; KAP1, SIM, SUMO-interacting motif; Siz, SAP and Miz-finger domain-containing protein; SP-RING, Siz/PIAS RING-finger domain;
KRAB-associated protein 1; Mms21, methyl methanesulfonate sensitivity protein 21; Pc2, polycomb group protein 2; PIAS, STUbL, SUMO-targeted ubiquitin ligase; SUMO, small ubiquitin-related modifier; Topors, topoisomerase I-binding RING
protein inhibitor of activated STAT; RanBP2, Ran binding protein 2; S, SUMO; S-1, SUMO-1; S-2/3, SUMO-2/3; Sae1, finger protein; U, ubiquitin; Ubc9, ubiquitin-conjugating enzyme E2 I (SUMO-conjugating enzyme); Ulp, ubiquitin-like-
SUMO-activating enzyme subunit 1 (E1); Sae2, SUMO-activating enzyme subunit 2 (E1); SENP, sentrin-specific protease; protein-specific protease.
© Journal of Cell Science 2009 (122, pp. 4249-4252)

(See poster insert)


4250 Journal of Cell Science 122 (23)

dynamic than the other SUMO paralogues, and These enzymes are structurally similar to E1 and finger domain (Siz) proteins in yeast and
its pattern of conjugation responds differently to E2 enzymes of ubiquitin, and they share many of protein inhibitor of activated STAT (PIAS)
heat shock and stress (Ayaydin and Dasso, 2004; the properties that have been demonstrated for proteins in vertebrates (Hochstrasser, 2001). In
Saitoh and Hinchey, 2000). those enzymes (Hochstrasser, 2009). The budding yeast, Siz1p and Siz2p are required for
Smt3p, SUMO-2 and SUMO-3 can form yeast SUMO E1 enzyme is a heterodimer most Smt3p conjugation (Johnson and Gupta,
conjugated chains through a single conserved consisting of Aos1p (also known as Sae1 in 2001; Takahashi et al., 2001). Other SP-RING
acceptor lysine (Bylebyl et al., 2003; Tatham vertebrates) and Uba2p (also known as Sae2 proteins, Zip3p and Mms21p, promote
et al., 2001). SUMO-1 does not have an in vertebrates), which show sequence similarity assembly of the synaptonemal complex
equivalent lysine residue, and thus probably to the N-terminus and C-terminus of the between homologous chromosomes during
does not act as a link in elongating chains monomeric ubiquitin E1 enzyme, respectively meiosis (Cheng et al., 2006) and DNA repair
in vivo. However, SUMO-1 might terminate (Johnson et al., 1997). Aos1p-Uba2p catalyzes (Potts, 2009), respectively. The five vertebrate
chains that are elongated through serial the formation of a high-energy thioester bond PIAS proteins (PIAS1, PIAS3, PIASx,
conjugation of SUMO-2/3 (Matic et al., 2008). between Uba2p and the SUMO C-terminus, PIASx and PIAS) have been implicated in
Notably, although SUMOylation does not seem with ATP hydrolysis to AMP and pyrophosphate many processes, including gene expression,
to rely upon the geometry of chain linkages to (Johnson et al., 1997; Lois and Lima, 2005). The signal transduction and genome maintenance
confer information, as ubiquitylation does activated SUMO is subsequently passed to a (Palvimo, 2007).
(Pickart and Fushman, 2004), SUMO cysteine in the active site of the E2 enzyme, Beyond their SP-RING domains, Siz/PIAS-
conjugates built from different paralogues or Ubc9, through an intermolecular thiol-transfer family members share additional conserved
with different chain lengths can specify distinct reaction. motifs, including an N-terminal scaffold
target fates, as discussed below. Residues of Ubc9 that are directly involved in attachment factor (SAF)-A/B, acinus, PIAS
the transfer of SUMO act to orient the lysine (SAP) motif, a PINIT motif, a SIM, and a
SUMO-interacting motifs of the target protein and to decrease its pKa, C-terminal domain that is rich in serine and
SUMO-interacting motifs (SIMs) play a central resulting in a higher occurrence of its activated, acidic amino acids (S/DE domain) (Palvimo,
role in both the enzymology of the SUMO de-protonated state (Yunus and Lima, 2006). 2007). The SAP domain directs the localization
Journal of Cell Science

pathway and in the fate of conjugated species. SUMO transfer from Ubc9 to some target of Siz/PIAS proteins to chromatin within the
The best-characterized class of SIM consists of a proteins can occur through at least two ligase- nucleus (Azuma et al., 2005; Palvimo, 2007).
hydrophobic core ([V/I]-x-[V/I]-[V/I]) flanked independent mechanisms. First, many Structural analysis of a Siz1 fragment that is
by a cluster of negatively charged amino acids SUMOylated lysines lie within a consensus sufficient for E3 activity in vitro shows that it
(Kerscher, 2007). The SIM hydrophobic core motif, -K-x-[D/E] (where  is an aliphatic has an elongated tripartite architecture, formed
can bind to an interaction surface on SUMO branched amino acid and x is any amino acid). by its N-terminal PINIT domain, SP-RING
proteins in a parallel or antiparallel orientation. Ubc9 can directly recognize this motif and domain and C-terminal domain, termed the
The acidic residues adjacent to the core might conjugate the lysine residue within it (Bernier- SP-CTD (Yunus and Lima, 2009). The SP-
contribute to the affinity, orientation or Villamor et al., 2002). Second, some SUMO RING and SP-CTD domains are required for
paralogue specificity of binding (Hecker et al., substrates contain SIMs that promote their own activation of the Ubc9-SUMO thioester,
2006; Meulmeester et al., 2008). A variant SIM conjugation (Meulmeester et al., 2008; Zhu whereas the PINIT domain directs
was recently defined within the transcriptional et al., 2008). These SIMs bind to the SUMO SUMOylation to the correct target lysine.
repressor CoREST1, consisting of [I/V/L]- moiety to which Ubc9 is attached, thereby
[D/E]-[I/V/L]-[D/E]-[I/V/L] with N-terminal increasing its local concentration and RanBP2
acidic residues (Ouyang et al., 2009). This SIM facilitating SUMOylation. Because SIMs show RanBP2 is a nuclear-pore protein that localizes
is highly selective for SUMO-2/3 binding, and paralogue preference, this mechanism allows to the cytoplasmic face of the pore. RanBP2
differs from previously identified SIMs because targets to be modified in a paralogue-selective possesses a domain called the internal repeat
its core lacks a hydrophobic residue at position manner. Notably, mammalian Ubc9 can itself be (IR) domain, which consists of two tandemly
4. Notably, the diversity of SIMs identified to SUMOylated on a nonconsensus lysine in its repeated sequences of around 50 residues (IR1
date is much less than the 16 known ubiquitin- N-terminal helix (Knipscheer et al., 2008). This and IR2), separated by a 24-residue spacer (M).
binding domains (Grabbe and Dikic, 2009); it is modification does not inhibit its activity per se, RanBP2 fragments containing the IR domain
reasonable to speculate that additional SIMs but alters its target preference, increasing the have SUMO ligase activity in vitro (Pichler
remain to be discovered. conjugation of substrates that contain SIMs, et al., 2002). Structural analysis of a RanBP2
which bind to the SUMO that is conjugated to fragment containing the IR1 and M domains
SUMO-processing, -activating and Ubc9. indicates that RanBP2 enhances Ubc9 activity
-conjugating enzymes without direct contacts to the target protein
Newly translated SUMO proteins are cleaved to SUMO ligases (Reverter and Lima, 2005). It has thus been
reveal C-terminal diglycine motifs. This SUMO ligases (E3 enzymes) facilitate the proposed that RanBP2 promotes SUMOylation
processing is mediated by a family of majority of SUMOylation under physiological by aligning the Ubc9-SUMO thioester complex
proteases known as ubiquitin-like-protein- conditions (Meulmeester et al., 2008). A number in an optimal configuration for substrate
specific proteases (Ulps) in yeast and of SUMO ligases have been described, most of interaction with the active site of Ubc9 and for
sentrin-specific proteases (SENPs) in mammals which seem to be specific to metazoans. catalysis. Notably, the IR domain of RanBP2
(Mukhopadhyay and Dasso, 2007). Ulps and binds extremely stably to Ubc9 and the
SENPs also mediate deSUMOylation (see Siz/PIAS-family proteins SUMO-1-conjugated form of RanGAP1,
below). All eukaryotes express proteins with Siz/PIAS the activating protein for the GTPase Ran
All SUMO paralogues share the same RING-finger-like domains (SP-RING (Matunis et al., 1998; Saitoh et al., 1998).
activating (E1) and conjugating (E2) enzymes. domains), which are known as SAP and Miz- Structural analysis yielded the puzzling result
Journal of Cell Science 122 (23) 4251

that this binding abolishes the ability of RanBP2 nuclear envelope and is encoded by an The fates of SUMOylated species
to promote multiple rounds of target essential gene (Li and Hochstrasser, 1999). The consequences of SUMOylation are diverse,
SUMOylation (Reverter and Lima, 2005). It Overexpression of processed Smt3p weakly including alteration of the activity, localization
will clearly be important to establish how this rescues ulp1 cells, but unprocessed Smt3p does and/or stability of the target protein (Geiss-
inhibition is overcome for RanBP2 to act as an not (Li and Hochstrasser, 1999), suggesting that Friedlander and Melchior, 2007). Frequently,
E3 enzyme in its physiological context. one essential function of Ulp1p is Smt3p these consequences result from recognition of
maturation. Ulp2p localizes in the nucleoplasm conjugated species by SIM-containing proteins.
Other SUMO ligases (Li and Hochstrasser, 2000) and is particularly SUMOylation might also cause the loss of
Additional proteins that have been reported as important for dismantling poly-Smt3p chains binding partners, or cause conformational
potential SUMO ligases include histone (Bylebyl et al., 2003). Although not essential for changes that alter the enzymatic activity of the
deacetylase 4 (HDAC4), KRAB-associated vegetative growth, Ulp2p has roles in target protein. Some SIM-mediated interactions
protein 1 (KPA1), Pc2 and Topors. chromosome segregation, meiotic development prevent deconjugation by limiting the access of
HDAC4 is a histone deacetylase that is a and recovery from cell-cycle checkpoint arrest Ulps/SENPs to the conjugated proteins. In cases
SUMOylation target. HDAC4 expression (Li and Hochstrasser, 2000). in which the interacting SIMs have intrinsic
enhances the SUMOylation of myocyte-specific Mammals have six SENPs: SENP1, SENP2, paralogue preference, they will selectively
enhancer factor 2 (MEF2), as well as other SENP3, SENP5, SENP6 and SENP7. SENP1-3 protect targets that are modified with the
targets (Geiss-Friedlander and Melchior, 2007; and SENP5 are more similar to Ulp1p than to preferred SUMO paralogue (Zhu et al., 2009).
Zhao et al., 2005). HDAC4 can bind to Ubc9, Ulp2p, whereas SENP6 and SENP7 are more Few SUMOylation targets show quantitative
suggesting that it acts as an E3 enzyme. It has Ulp2-like (Mukhopadhyay and Dasso, 2007). modification. Notably, SUMOylation can play
alternatively been proposed that HDAC4 SENP1 and SENP2 localize to the nuclear an important regulatory role even under these
enhances SUMOylation by other means, such envelope and have processing and circumstances (Geiss-Friedlander and Melchior,
as promoting the phosphorylation of target deconjugation activity for both SUMO-1 and 2007). This might be explained by the
proteins at sites adjacent to conjugated lysine SUMO-2/3. By contrast, all other SENPs have a observation that SUMOylation can promote
residues (Yang and Gregoire, 2006). strong preference for SUMO-2/3. SENP3 and the assembly of protein complexes, such as in
Journal of Cell Science

The human co-repressor KRAB-associated SENP5 localize in nucleoli and catalyze transcriptionally repressed chromatin, that
protein 1 (KAP1) possesses PHD-finger domains SUMO-2/3 processing and deconjugation (Di remain stable despite subsequent
that catalyze intramolecular SUMOylation of an Bacco et al., 2006; Gong and Yeh, 2006). deSUMOylation (Geiss-Friedlander and
adjacent KAP1 bromodomain (Peng and Similar to Ulp1p (Panse et al., 2006), SENP3 Melchior, 2007). Additionally, SUMOylation
Wysocka, 2008). SUMOylation stabilizes the and SENP5 have important roles in ribosome might function within the catalytic cycle of
association of the bromodomain with biogenesis (Yun et al., 2008). SENP6 and targets, facilitating enzymatic turnover
the chromatin modifiers, thus promoting the SENP7 localize within the nucleoplasm and are (Hardeland et al., 2002). In both of these cases,
establishment of gene silencing. Structural implicated in the editing of poly-SUMO chains SUMOylated species are transient intermediates
analysis suggests that the PHD finger and the (Lima and Reverter, 2008; Mukhopadhyay that facilitate stable changes in target proteins.
bromodomain cooperate as an integrated unit to et al., 2006; Shen et al., 2009).
recruit Ubc9 and facilitate SUMOylation (Zeng The sites of SENP1, SENP2 and Ulp1p that are Crosstalk between the SUMO and
et al., 2008). engaged during processing or deconjugation are ubiquitin pathways
Mammalian Pc2 is a polycomb-group shallow clefts lined with conserved amino acids A particularly exciting development in this field
protein that can act as a SUMO ligase for the (Mossessova and Lima, 2000; Reverter and has revealed an important point of crosstalk
transcriptional co-repressor CtBP (Wotton and Lima, 2004; Shen et al., 2006b). In both reactions, between the SUMO and ubiquitin pathways
Merrill, 2007). Pc2 can bind to both Ubc9 and its the C-terminus of SUMO lies within these clefts (Hunter and Sun, 2008): a subset of targets
conjugation targets, and it seems to have a rather as an elongated strand, and conserved become conjugated with multiple SUMOs, and
limited spectrum of targets. tryptophans and other adjacent residues of Ulp1p, can be recognized by SUMO-targeted ubiquitin
Topors is a RING-finger protein that binds SENP1 and SENP2 clamp the diglycine motif of ligases (STUbLs), causing the proteasomal
DNA topoisomerase I and p53. It possesses both SUMO in a hydrophobic ‘tunnel’. During degradation of these targets. It is currently
RING-finger-dependent ubiquitin ligase deconjugation, such binding requires minimal believed that STUbLs operate primarily through
activity and RING-finger-independent SUMO structural distortion of the target protein, which recognition of poly-SUMO chains, although it
ligase activity (Weger et al., 2005). Topors has a explains how Ulps/SENPs can deconjugate many remains possible that they might recognize some
SIM (Hecker et al., 2006) and acts as a SUMO SUMOylated species with only modest target targets that are mono-SUMOylated at numerous
ligase in vitro (Hammer et al., 2007). specificity. In the SUMO processing reaction, sites.
Ulps/SENPs induce the isomerization of the Rfp1p and Rfp2p are fission-yeast RING-
SUMO-deconjugating enzymes scissile peptide bond, resulting in a 90° kink in the finger proteins that possess N-terminal SIMs
Ulps/SENPs are responsible both for processing SUMO C-terminal tail (Reverter and Lima, 2006; (Sun et al., 2007). They are genetically
SUMO peptides and for deconjugating Shen et al., 2006a). In deconjugation reactions, redundant and there is no visible phenotype for
SUMOylated species (Hay, 2007; Ulps/SENPs induce the scissile isopeptide bond loss of either gene encoding these proteins.
Mukhopadhyay and Dasso, 2007). Ulps/SENPs between the C-terminus of SUMO and the However, cells must possess at least one of these
share a conserved ~200-amino-acid catalytic -amine group of the lysine residue of the target proteins for growth and genome stability. Both
domain that is typically found near their protein to adopt a cis configuration, resulting in a Rfp1p and Rfp2p heterodimerize with the Slx8p
C-terminus. similar 90° kink (Reverter and Lima, 2006; Shen protein, a RING-finger ubiquitin ligase.
There are two Ulps in budding yeast: Ulp1p et al., 2006a). For both peptide and amide bonds, Together, they mediate the ubiquitylation of
and Ulp2p (Li and Hochstrasser, 1999; Li and the kinked cis conformations facilitate hydrolysis poly-SUMOylated targets, resulting in their
Hochstrasser, 2000). Ulp1p localizes to the of the bond. proteasomal destruction. The Slx5p-Slx8p
4252 Journal of Cell Science 122 (23)

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Journal of Cell Science

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This work was supported through Eunice Kennedy ubiquitin-like modifier polymerization sites by high accuracy proteomics. Mol. Cell Proteomics 5, 2298-2310.
Shriver National Institute of Child Health and Human mass spectrometry and an in vitro to in vivo strategy. Mol. Cell Weger, S., Hammer, E. and Heilbronn, R. (2005). Topors acts
Proteomics 7, 132-144. as a SUMO-1 E3 ligase for p53 in vitro and in vivo. FEBS Lett.
Development Intramural funds (Z01 HD001902).
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