SUMOylation and DeSUMOylation at a Glance - Journal of Cell ...

Journal of Cell Science
Cell Science at a Glance
SUMOylation and
deSUMOylation at a
glance
Yonggang Wang and
Mary Dasso*
Laboratory of Gene Regulation and Development,
National Institute of Child Health and Human
Development, Bethesda, MD 20892, USA
*Author for correspondence (mdasso@helix.nih.gov)
Journal of Cell Science 122, 4249-4252
Published by The Company of Biologists 2009
doi:10.1242/jcs.050542
Small ubiquitin-related modifiers (SUMOs) are
ubiquitin-like polypeptides that become
covalently conjugated to cellular proteins in a
manner similar to ubiquitylation (Johnson,
2004). More than 1000 proteins have been
identified as potential SUMO-conjugation
(SUMOylation) targets (Hochstrasser, 2009),
jcs.biologists.org
Key steps and components in the SUMO pathway
1.
2.
Cleavage SUMO
of SUMO activation
C-terminus (linkage to
E1 enzyme)
Aos1
E3s Ulp/SENP
Ulp/SENP
ATP
SH
AMP+PPi
Aos1
SH
Uba2 SH Ubc9
K
Target S
S S Uba2 S S S S
K
Target
Aos1
Uba2 SH Ubc9
Abbreviations: DUB, deubiquitylating enzyme; E3s, E3 ligases; HDAC4, histone deacetylase 4; IR, internal repeat; KAP1,
KRAB-associated protein 1; Mms21, methyl methanesulfonate sensitivity protein 21; Pc2, polycomb group protein 2; PIAS,
protein inhibitor of activated STAT; RanBP2, Ran binding protein 2; S, SUMO; S-1, SUMO-1; S-2/3, SUMO-2/3; Sae1,
SUMO-activating enzyme subunit 1 (E1); Sae2, SUMO-activating enzyme subunit 2 (E1); SENP, sentrin-specific protease;
and this pathway has been implicated in
controlling many aspects of cell physiology,
including cell-cycle regulation, transcription,
nucleocytoplasmic transport, DNA replication
and repair, chromosome dynamics,
apoptosis, and ribosome biogenesis.
Both SUMOylation and deSUMOylation
(SUMO deconjugation) are highly dynamic
processes. This poster article discusses the
enzymes that mediate SUMOylation and
deSUMOylation, concentrating on their
mechanisms of action. Although it is not
possible to discuss individual SUMOylated
targets in detail, we will mention emerging
paradigms that explain how SUMOylation
might direct the fate of target proteins.
SUMO paralogues
Yeast express a single SUMO paralogue, called
Smt3p in Saccharomyces cerevisiae.
Mammalian cells express three major SUMO
paralogues, called SUMO-1, SUMO-2 and
SUMOylation and DeSUMOylation at a Glance
4.
SUMOylation
of target
(E3-dependent
or -independent;
see below)
K
Target
Mammals S. cerevisiae S. pombe
Small ubiquitin-related modifiers SUMO-1, SUMO-2, SUMO-3 Smt3p Pmt3p
Activating enzyme (E1)
Aos1 (Sae1)-Uba2 (Sae2)
Aos1p-Uba2p Rad31p-Fub2p
Conjugating enzyme (E2) Ubc9
Ubc9p Hus5p
SP-RING-type E3 ligases PIAS1, PIAS3, PIASxα (ARIP3), Siz1p (UII1p), Pli1p, Nse2p
PIASxβ (Miz1), PIASγ (PIAS4), Siz2p (Nfi1p),
Mms21 (Nse2)
Mms21p
(Nse2p), Zip3p
IR E3 ligase
Other E3 ligases
Protease (Ulp/SENP)
3.
SUMO
transfer to
E2 enzyme
3.
DeSUMOylation
(see below)
RanBP2 (Nup358)
HDAC4, KAP1, Pc2, Topors
SENP1 (SuPr-2), SENP2 (SMT3IP2, UIp1p (Nib1p), Ulp1p, Ulp2p
SSP3, Axam2), SENP3 (SMT3IP1), Ulp2p (Smt4p)
SENP5 (SMT3IP3), SENP6 (SSP1,
SUSP1), SENP7
S
Yonggang Wang and Mary Dasso
Target
SUMO-1
E1, E2, E3
K
Ulp/SENP
Ulp/SENP
Ulp/SENP
SUMOylation confers multiple fates
Ubiquitin
E1, E2, STUbL
SIM, SUMO-interacting motif; Siz, SAP and Miz-finger domain-containing protein; SP-RING, Siz/PIAS RING-finger domain;
STUbL, SUMO-targeted ubiquitin ligase; SUMO, small ubiquitin-related modifier; Topors, topoisomerase I-binding RING
finger protein; U, ubiquitin; Ubc9, ubiquitin-conjugating enzyme E2 I (SUMO-conjugating enzyme); Ulp, ubiquitin-likeprotein-specific
protease.
4249
SUMO-3. SUMO-2 and SUMO-3 are ~95%
identical to each other. In most contexts,
SUMO-2 and SUMO-3 cannot be distinguished,
and here we collectively refer to them as
SUMO-2/3. SUMO-2 and SUMO-3 are each
~45% identical to SUMO-1, and all mammalian
paralogues are ~ 45% identical to Smt3p.
There are several important differences
between the mammalian SUMO paralogues.
First, some SUMO targets are conjugated only to
SUMO-1, others only to SUMO-2/3, and still
others to all SUMO paralogues (Vertegaal
et al., 2006). Second, the overall cellular
concentration of SUMO-2/3 is greater than that of
SUMO-1, as is the pool of free protein available
for conjugation (Saitoh and Hinchey, 2000). It is
thus likely that the bulk of SUMOylation
involves SUMO-2/3. Third, SUMO-1 and
SUMO-2/3 show different subcellular
localization patterns (Ayaydin and Dasso, 2004;
Zhang et al., 2008). Fourth, photobleaching
experiments suggest that SUMO-1 is less
E3-dependent (Siz/PIAS-mediated) SUMOylation E3-independent (SIM-mediated) SUMOylation
Mechanism of SUMO deconjugation by Ulp/SENP
O
Gly
S S
Cys
Ubc9
Ubc9-bound
SUMO
Siz/
PIAS
Ubc9
Ubc9
Ubc9
Free target Siz/PIAS and Ubc9bound
substrate
Ubc9
Ubc9
SUMO-2/3
E1, E2, E3
Conjugate Free target SIM-mediated
bound intermediate
S
S-1
K
S-2/3
K
S-2/3n
Ulp/SENP
K
Target
SUMO-1
E1, E2, E3
O
Gly
S
Cys
Enzyme-bound
substrate
S-2/3
K
Target
SUMO-2/3n
E1, E2, E3
S-2/3
K
S-2/3n
K
Target
Siz/
O
O
PIAS
O
Gly
S S
Gly
Ubc9
S S
Gly O
Gly
Cys
Cys
S
S S
NH
Cys
Siz/
Siz/
NH2
K
PIAS
PIAS
K
SIM K NH2
NH2
Target
SIM K NH2 Target
K
Target
Target
Target
HS
Cys
SIM
Target
K NH2
O
SIM K NH
Target
S
S
Gly
S
Cys
O
Ubc9
S-1
K
Target
HS
Cys
Ubc9
DUB
Conjugate
Gly
Un
a. Blocking a binding site
Interactor
K
Target arget
SUMOylation
S
K
Target Ta T rget
U
U
DeSUMOylation
b. Creation of additional binding site
Interactor
Interactor
SIM
SIM
S
K SUMOylation
K
Target
Target
DeSUMOylation
c. Conformation alteration
K SUMOylation
Target
DeSUMOylation
Un
S-2/3
U S-2/3
S-2/3
S-2/3n
K K
Target
S
Gly
O
NH
K
Target
Substrate
(trans conformation)
Ulp/SENP
HS-Cys
Free enzyme
S
K
Target
U
Interactor
U
U
S
O Gly
OH
Ulp/SENP S
O Gly
S-Cys
NH
K
Target
Enzyme-bound substrate
(cis conformation)
Cell-cycle regulation
Gene transcription
Nucleocytoplasmic transport
DNA replication and repair
Chromosome dynamics
Apoptosis
Ribosome biogenesis
Others
S-2/3
S-2/3
T r e
S-2/3
a
g
t
S-2/3n
Proteasome-mediated
degradation
NH2
K
Target
Ulp/SENP S
O Gly
S-Cys
Thioester intermediate
H2O
Ulp/SENP S
O Gly
OH HS-Cys
Product-bound enzyme
© Journal of Cell Science 2009 (122, pp. 4249-4252)
(See poster insert)

Journal of Cell Science
4250
Journal of Cell Science 122 (23)
dynamic than the other SUMO paralogues, and
its pattern of conjugation responds differently to
heat shock and stress (Ayaydin and Dasso, 2004;
Saitoh and Hinchey, 2000).
Smt3p, SUMO-2 and SUMO-3 can form
conjugated chains through a single conserved
acceptor lysine (Bylebyl et al., 2003; Tatham
et al., 2001). SUMO-1 does not have an
equivalent lysine residue, and thus probably
does not act as a link in elongating chains
in vivo. However, SUMO-1 might terminate
chains that are elongated through serial
conjugation of SUMO-2/3 (Matic et al., 2008).
Notably, although SUMOylation does not seem
to rely upon the geometry of chain linkages to
confer information, as ubiquitylation does
(Pickart and Fushman, 2004), SUMO
conjugates built from different paralogues or
with different chain lengths can specify distinct
target fates, as discussed below.
SUMO-interacting motifs
SUMO-interacting motifs (SIMs) play a central
role in both the enzymology of the SUMO
pathway and in the fate of conjugated species.
The best-characterized class of SIM consists of a
hydrophobic core ([V/I]-x-[V/I]-[V/I]) flanked
by a cluster of negatively charged amino acids
(Kerscher, 2007). The SIM hydrophobic core
can bind to an interaction surface on SUMO
proteins in a parallel or antiparallel orientation.
The acidic residues adjacent to the core might
contribute to the affinity, orientation or
paralogue specificity of binding (Hecker et al.,
2006; Meulmeester et al., 2008). A variant SIM
was recently defined within the transcriptional
repressor CoREST1, consisting of [I/V/L]-
[D/E]-[I/V/L]-[D/E]-[I/V/L] with N-terminal
acidic residues (Ouyang et al., 2009). This SIM
is highly selective for SUMO-2/3 binding, and
differs from previously identified SIMs because
its core lacks a hydrophobic residue at position
4. Notably, the diversity of SIMs identified to
date is much less than the 16 known ubiquitinbinding
domains (Grabbe and Dikic, 2009); it is
reasonable to speculate that additional SIMs
remain to be discovered.
SUMO-processing, -activating and
-conjugating enzymes
Newly translated SUMO proteins are cleaved to
reveal C-terminal diglycine motifs. This
processing is mediated by a family of
proteases known as ubiquitin-like-proteinspecific
proteases (Ulps) in yeast and
sentrin-specific proteases (SENPs) in mammals
(Mukhopadhyay and Dasso, 2007). Ulps and
SENPs also mediate deSUMOylation (see
below).
All SUMO paralogues share the same
activating (E1) and conjugating (E2) enzymes.
These enzymes are structurally similar to E1 and
E2 enzymes of ubiquitin, and they share many of
the properties that have been demonstrated for
those enzymes (Hochstrasser, 2009). The
yeast SUMO E1 enzyme is a heterodimer
consisting of Aos1p (also known as Sae1 in
vertebrates) and Uba2p (also known as Sae2
in vertebrates), which show sequence similarity
to the N-terminus and C-terminus of the
monomeric ubiquitin E1 enzyme, respectively
(Johnson et al., 1997). Aos1p-Uba2p catalyzes
the formation of a high-energy thioester bond
between Uba2p and the SUMO C-terminus,
with ATP hydrolysis to AMP and pyrophosphate
(Johnson et al., 1997; Lois and Lima, 2005). The
activated SUMO is subsequently passed to a
cysteine in the active site of the E2 enzyme,
Ubc9, through an intermolecular thiol-transfer
reaction.
Residues of Ubc9 that are directly involved in
the transfer of SUMO act to orient the lysine
of the target protein and to decrease its pKa,
resulting in a higher occurrence of its activated,
de-protonated state (Yunus and Lima, 2006).
SUMO transfer from Ubc9 to some target
proteins can occur through at least two ligaseindependent
mechanisms. First, many
SUMOylated lysines lie within a consensus
motif, �-K-x-[D/E] (where � is an aliphatic
branched amino acid and x is any amino acid).
Ubc9 can directly recognize this motif and
conjugate the lysine residue within it (Bernier-
Villamor et al., 2002). Second, some SUMO
substrates contain SIMs that promote their own
conjugation (Meulmeester et al., 2008; Zhu
et al., 2008). These SIMs bind to the SUMO
moiety to which Ubc9 is attached, thereby
increasing its local concentration and
facilitating SUMOylation. Because SIMs show
paralogue preference, this mechanism allows
targets to be modified in a paralogue-selective
manner. Notably, mammalian Ubc9 can itself be
SUMOylated on a nonconsensus lysine in its
N-terminal helix (Knipscheer et al., 2008). This
modification does not inhibit its activity per se,
but alters its target preference, increasing the
conjugation of substrates that contain SIMs,
which bind to the SUMO that is conjugated to
Ubc9.
SUMO ligases
SUMO ligases (E3 enzymes) facilitate the
majority of SUMOylation under physiological
conditions (Meulmeester et al., 2008). A number
of SUMO ligases have been described, most of
which seem to be specific to metazoans.
Siz/PIAS-family proteins
All eukaryotes express proteins with Siz/PIAS
RING-finger-like domains (SP-RING
domains), which are known as SAP and Miz-
finger domain (Siz) proteins in yeast and
protein inhibitor of activated STAT (PIAS)
proteins in vertebrates (Hochstrasser, 2001). In
budding yeast, Siz1p and Siz2p are required for
most Smt3p conjugation (Johnson and Gupta,
2001; Takahashi et al., 2001). Other SP-RING
proteins, Zip3p and Mms21p, promote
assembly of the synaptonemal complex
between homologous chromosomes during
meiosis (Cheng et al., 2006) and DNA repair
(Potts, 2009), respectively. The five vertebrate
PIAS proteins (PIAS1, PIAS3, PIASx�,
PIASx� and PIAS�) have been implicated in
many processes, including gene expression,
signal transduction and genome maintenance
(Palvimo, 2007).
Beyond their SP-RING domains, Siz/PIASfamily
members share additional conserved
motifs, including an N-terminal scaffold
attachment factor (SAF)-A/B, acinus, PIAS
(SAP) motif, a PINIT motif, a SIM, and a
C-terminal domain that is rich in serine and
acidic amino acids (S/DE domain) (Palvimo,
2007). The SAP domain directs the localization
of Siz/PIAS proteins to chromatin within the
nucleus (Azuma et al., 2005; Palvimo, 2007).
Structural analysis of a Siz1 fragment that is
sufficient for E3 activity in vitro shows that it
has an elongated tripartite architecture, formed
by its N-terminal PINIT domain, SP-RING
domain and C-terminal domain, termed the
SP-CTD (Yunus and Lima, 2009). The SP-
RING and SP-CTD domains are required for
activation of the Ubc9-SUMO thioester,
whereas the PINIT domain directs
SUMOylation to the correct target lysine.
RanBP2
RanBP2 is a nuclear-pore protein that localizes
to the cytoplasmic face of the pore. RanBP2
possesses a domain called the internal repeat
(IR) domain, which consists of two tandemly
repeated sequences of around 50 residues (IR1
and IR2), separated by a 24-residue spacer (M).
RanBP2 fragments containing the IR domain
have SUMO ligase activity in vitro (Pichler
et al., 2002). Structural analysis of a RanBP2
fragment containing the IR1 and M domains
indicates that RanBP2 enhances Ubc9 activity
without direct contacts to the target protein
(Reverter and Lima, 2005). It has thus been
proposed that RanBP2 promotes SUMOylation
by aligning the Ubc9-SUMO thioester complex
in an optimal configuration for substrate
interaction with the active site of Ubc9 and for
catalysis. Notably, the IR domain of RanBP2
binds extremely stably to Ubc9 and the
SUMO-1-conjugated form of RanGAP1,
the activating protein for the GTPase Ran
(Matunis et al., 1998; Saitoh et al., 1998).
Structural analysis yielded the puzzling result

Journal of Cell Science
that this binding abolishes the ability of RanBP2
to promote multiple rounds of target
SUMOylation (Reverter and Lima, 2005). It
will clearly be important to establish how this
inhibition is overcome for RanBP2 to act as an
E3 enzyme in its physiological context.
Other SUMO ligases
Additional proteins that have been reported as
potential SUMO ligases include histone
deacetylase 4 (HDAC4), KRAB-associated
protein 1 (KPA1), Pc2 and Topors.
HDAC4 is a histone deacetylase that is a
SUMOylation target. HDAC4 expression
enhances the SUMOylation of myocyte-specific
enhancer factor 2 (MEF2), as well as other
targets (Geiss-Friedlander and Melchior, 2007;
Zhao et al., 2005). HDAC4 can bind to Ubc9,
suggesting that it acts as an E3 enzyme. It has
alternatively been proposed that HDAC4
enhances SUMOylation by other means, such
as promoting the phosphorylation of target
proteins at sites adjacent to conjugated lysine
residues (Yang and Gregoire, 2006).
The human co-repressor KRAB-associated
protein 1 (KAP1) possesses PHD-finger domains
that catalyze intramolecular SUMOylation of an
adjacent KAP1 bromodomain (Peng and
Wysocka, 2008). SUMOylation stabilizes the
association of the bromodomain with
the chromatin modifiers, thus promoting the
establishment of gene silencing. Structural
analysis suggests that the PHD finger and the
bromodomain cooperate as an integrated unit to
recruit Ubc9 and facilitate SUMOylation (Zeng
et al., 2008).
Mammalian Pc2 is a polycomb-group
protein that can act as a SUMO ligase for the
transcriptional co-repressor CtBP (Wotton and
Merrill, 2007). Pc2 can bind to both Ubc9 and its
conjugation targets, and it seems to have a rather
limited spectrum of targets.
Topors is a RING-finger protein that binds
DNA topoisomerase I and p53. It possesses both
RING-finger-dependent ubiquitin ligase
activity and RING-finger-independent SUMO
ligase activity (Weger et al., 2005). Topors has a
SIM (Hecker et al., 2006) and acts as a SUMO
ligase in vitro (Hammer et al., 2007).
SUMO-deconjugating enzymes
Ulps/SENPs are responsible both for processing
SUMO peptides and for deconjugating
SUMOylated species (Hay, 2007;
Mukhopadhyay and Dasso, 2007). Ulps/SENPs
share a conserved ~200-amino-acid catalytic
domain that is typically found near their
C-terminus.
There are two Ulps in budding yeast: Ulp1p
and Ulp2p (Li and Hochstrasser, 1999; Li and
Hochstrasser, 2000). Ulp1p localizes to the
nuclear envelope and is encoded by an
essential gene (Li and Hochstrasser, 1999).
Overexpression of processed Smt3p weakly
rescues �ulp1 cells, but unprocessed Smt3p does
not (Li and Hochstrasser, 1999), suggesting that
one essential function of Ulp1p is Smt3p
maturation. Ulp2p localizes in the nucleoplasm
(Li and Hochstrasser, 2000) and is particularly
important for dismantling poly-Smt3p chains
(Bylebyl et al., 2003). Although not essential for
vegetative growth, Ulp2p has roles in
chromosome segregation, meiotic development
and recovery from cell-cycle checkpoint arrest
(Li and Hochstrasser, 2000).
Mammals have six SENPs: SENP1, SENP2,
SENP3, SENP5, SENP6 and SENP7. SENP1-3
and SENP5 are more similar to Ulp1p than to
Ulp2p, whereas SENP6 and SENP7 are more
Ulp2-like (Mukhopadhyay and Dasso, 2007).
SENP1 and SENP2 localize to the nuclear
envelope and have processing and
deconjugation activity for both SUMO-1 and
SUMO-2/3. By contrast, all other SENPs have a
strong preference for SUMO-2/3. SENP3 and
SENP5 localize in nucleoli and catalyze
SUMO-2/3 processing and deconjugation (Di
Bacco et al., 2006; Gong and Yeh, 2006).
Similar to Ulp1p (Panse et al., 2006), SENP3
and SENP5 have important roles in ribosome
biogenesis (Yun et al., 2008). SENP6 and
SENP7 localize within the nucleoplasm and are
implicated in the editing of poly-SUMO chains
(Lima and Reverter, 2008; Mukhopadhyay
et al., 2006; Shen et al., 2009).
The sites of SENP1, SENP2 and Ulp1p that are
engaged during processing or deconjugation are
shallow clefts lined with conserved amino acids
(Mossessova and Lima, 2000; Reverter and
Lima, 2004; Shen et al., 2006b). In both reactions,
the C-terminus of SUMO lies within these clefts
as an elongated strand, and conserved
tryptophans and other adjacent residues of Ulp1p,
SENP1 and SENP2 clamp the diglycine motif of
SUMO in a hydrophobic ‘tunnel’. During
deconjugation, such binding requires minimal
structural distortion of the target protein, which
explains how Ulps/SENPs can deconjugate many
SUMOylated species with only modest target
specificity. In the SUMO processing reaction,
Ulps/SENPs induce the isomerization of the
scissile peptide bond, resulting in a 90° kink in the
SUMO C-terminal tail (Reverter and Lima, 2006;
Shen et al., 2006a). In deconjugation reactions,
Ulps/SENPs induce the scissile isopeptide bond
between the C-terminus of SUMO and the
�-amine group of the lysine residue of the target
protein to adopt a cis configuration, resulting in a
similar 90° kink (Reverter and Lima, 2006; Shen
et al., 2006a). For both peptide and amide bonds,
the kinked cis conformations facilitate hydrolysis
of the bond.
Journal of Cell Science 122 (23)
4251
The fates of SUMOylated species
The consequences of SUMOylation are diverse,
including alteration of the activity, localization
and/or stability of the target protein (Geiss-
Friedlander and Melchior, 2007). Frequently,
these consequences result from recognition of
conjugated species by SIM-containing proteins.
SUMOylation might also cause the loss of
binding partners, or cause conformational
changes that alter the enzymatic activity of the
target protein. Some SIM-mediated interactions
prevent deconjugation by limiting the access of
Ulps/SENPs to the conjugated proteins. In cases
in which the interacting SIMs have intrinsic
paralogue preference, they will selectively
protect targets that are modified with the
preferred SUMO paralogue (Zhu et al., 2009).
Few SUMOylation targets show quantitative
modification. Notably, SUMOylation can play
an important regulatory role even under these
circumstances (Geiss-Friedlander and Melchior,
2007). This might be explained by the
observation that SUMOylation can promote
the assembly of protein complexes, such as in
transcriptionally repressed chromatin, that
remain stable despite subsequent
deSUMOylation (Geiss-Friedlander and
Melchior, 2007). Additionally, SUMOylation
might function within the catalytic cycle of
targets, facilitating enzymatic turnover
(Hardeland et al., 2002). In both of these cases,
SUMOylated species are transient intermediates
that facilitate stable changes in target proteins.
Crosstalk between the SUMO and
ubiquitin pathways
A particularly exciting development in this field
has revealed an important point of crosstalk
between the SUMO and ubiquitin pathways
(Hunter and Sun, 2008): a subset of targets
become conjugated with multiple SUMOs, and
can be recognized by SUMO-targeted ubiquitin
ligases (STUbLs), causing the proteasomal
degradation of these targets. It is currently
believed that STUbLs operate primarily through
recognition of poly-SUMO chains, although it
remains possible that they might recognize some
targets that are mono-SUMOylated at numerous
sites.
Rfp1p and Rfp2p are fission-yeast RINGfinger
proteins that possess N-terminal SIMs
(Sun et al., 2007). They are genetically
redundant and there is no visible phenotype for
loss of either gene encoding these proteins.
However, cells must possess at least one of these
proteins for growth and genome stability. Both
Rfp1p and Rfp2p heterodimerize with the Slx8p
protein, a RING-finger ubiquitin ligase.
Together, they mediate the ubiquitylation of
poly-SUMOylated targets, resulting in their
proteasomal destruction. The Slx5p-Slx8p

Journal of Cell Science
4252
Journal of Cell Science 122 (23)
heterodimer acts similarly in budding yeast
(Hunter and Sun, 2008). The functions of Rfp1
and/or Rfp2 and Slx8 are performed by a single
protein in human cells, RING-finger protein 4
(RNF4), which is the only confirmed
mammalian STUbL (Sun et al., 2007).
Perspectives
Findings during the last 5 or 6 years have
provided a much more sophisticated
understanding of the SUMOylation pathway,
revealing some aspects that are unique to this
pathway and others that are probably common
to pathways involving all ubiquitin-like
proteins. However, the picture of SUMOylation
is not yet complete, and we expect that studies of
the SUMO pathway may yet hold more
surprises. In particular, we look forward to
future findings regarding the mechanisms of
SUMO ligases and the possibility that additional
SIMs remain to be discovered. Finally, we still
have much to learn regarding the biological
functions of this pathway and its interaction with
ubiquitin and other regulatory pathways.
This work was supported through Eunice Kennedy
Shriver National Institute of Child Health and Human
Development Intramural funds (Z01 HD001902).
Deposited in PMC for release after 12 months.
References
Ayaydin, F. and Dasso, M. (2004). Distinct in vivo dynamics of
vertebrate SUMO paralogues. Mol. Biol. Cell 15, 5208-5218.
Azuma, Y., Arnaoutov, A., Anan, T. and Dasso, M. (2005).
PIASy mediates SUMO-2 conjugation of Topoisomerase-II on
mitotic chromosomes. EMBO J. 24, 2172-2182.
Bernier-Villamor, V., Sampson, D. A., Matunis, M. J. and
Lima, C. D. (2002). Structural basis for E2-mediated SUMO
conjugation revealed by a complex between ubiquitinconjugating
enzyme Ubc9 and RanGAP1. Cell 108, 345-356.
Bylebyl, G. R., Belichenko, I. and Johnson, E. S. (2003). The
SUMO isopeptidase Ulp2 prevents accumulation of SUMO
chains in yeast. J. Biol. Chem. 278, 44113-44120.
Cheng, C. H., Lo, Y. H., Liang, S. S., Ti, S. C., Lin, F. M., Yeh,
C. H., Huang, H. Y. and Wang, T. F. (2006). SUMO
modifications control assembly of synaptonemal complex and
polycomplex in meiosis of Saccharomyces cerevisiae. Genes Dev.
20, 2067-2081.
Di Bacco, A., Ouyang, J., Lee, H. Y., Catic, A., Ploegh, H. and
Gill, G. (2006). The SUMO-specific protease SENP5 is required
for cell division. Mol. Cell. Biol. 26, 4489-4498.
Geiss-Friedlander, R. and Melchior, F. (2007). Concepts in
sumoylation: a decade on. Nat. Rev Mol. Cell. Biol. 8, 947-956.
Gong, L. and Yeh, E. T. (2006). Characterization of a family of
nucleolar SUMO-specific proteases with preference for SUMO-
2 or SUMO-3. J. Biol. Chem. 281, 15869-15877.
Grabbe, C. and Dikic, I. (2009). Functional roles of ubiquitinlike
domain (ULD) and ubiquitin-binding domain (UBD)
containing proteins. Chem. Rev. 109, 1481-1494.
Hammer, E., Heilbronn, R. and Weger, S. (2007). The E3 ligase
Topors induces the accumulation of polysumoylated forms of
DNA topoisomerase I in vitro and in vivo. FEBS Lett. 581, 5418-
5424.
Hardeland, U., Steinacher, R., Jiricny, J. and Schar, P. (2002).
Modification of the human thymine-DNA glycosylase by
ubiquitin-like proteins facilitates enzymatic turnover. EMBO J.
21, 1456-1464.
Hay, R. T. (2007). SUMO-specific proteases: a twist in the tail.
Trends Cell Biol. 17, 370-376.
Hecker, C. M., Rabiller, M., Haglund, K., Bayer, P. and Dikic,
I. (2006). Specification of SUMO1- and SUMO2-interacting
motifs. J. Biol. Chem. 281, 16117-16127.
Hochstrasser, M. (2001). SP-RING for SUMO: new functions
bloom for a ubiquitin-like protein. Cell 107, 5-8.
Hochstrasser, M. (2009). Origin and function of ubiquitin-like
proteins. Nature 458, 422-429.
Hunter, T. and Sun, H. (2008). Crosstalk between the SUMO
and ubiquitin pathways. Ernst Schering Found. Symp. Proc. 1-16.
Johnson, E. S. (2004). Protein modification by SUMO. Annu.
Rev. Biochem. 73, 355-382.
Johnson, E. S. and Gupta, A. A. (2001). An E3-like factor that
promotes SUMO conjugation to the yeast septins. Cell 106, 735-
744.
Johnson, E. S., Schwienhorst, I., Dohmen, R. J. and Blobel,
G. (1997). The ubiquitin-like protein Smt3p is activated for
conjugation to other proteins by an Aos1p/Uba2p heterodimer.
EMBO J. 16, 5509-5519.
Kerscher, O. (2007). SUMO junction-what’s your function? New
insights through SUMO-interacting motifs. EMBO Rep. 8, 550-
555.
Knipscheer, P., Flotho, A., Klug, H., Olsen, J. V., van Dijk, W.
J., Fish, A., Johnson, E. S., Mann, M., Sixma, T. K. and
Pichler, A. (2008). Ubc9 sumoylation regulates SUMO target
discrimination. Mol. Cell 31, 371-382.
Li, S. J. and Hochstrasser, M. (1999). A new protease required
for cell-cycle progression in yeast. Nature 398, 246-251.
Li, S. J. and Hochstrasser, M. (2000). The yeast ULP2 (SMT4)
gene encodes a novel protease specific for the ubiquitin-like Smt3
protein. Mol. Cell. Biol. 20, 2367-2377.
Lima, C. D. and Reverter, D. (2008). Structure of the human
SENP7 catalytic domain and poly-SUMO deconjugation
activities for SENP6 and SENP7. J. Biol. Chem. 283, 32045-
32055.
Lois, L. M. and Lima, C. D. (2005). Structures of the SUMO
E1 provide mechanistic insights into SUMO activation and E2
recruitment to E1. EMBO J. 24, 439-451.
Matic, I., van Hagen, M., Schimmel, J., Macek, B., Ogg, S. C.,
Tatham, M. H., Hay, R. T., Lamond, A. I., Mann, M. and
Vertegaal, A. C. (2008). In vivo identification of human small
ubiquitin-like modifier polymerization sites by high accuracy
mass spectrometry and an in vitro to in vivo strategy. Mol. Cell
Proteomics 7, 132-144.
Matunis, M. J., Wu, J. and Blobel, G. (1998). SUMO-1
modification and its role in targeting the Ran GTPase-activating
protein, RanGAP1, to the nuclear pore complex. J. Cell Biol. 140,
499-509.
Meulmeester, E., Kunze, M., Hsiao, H. H., Urlaub, H. and
Melchior, F. (2008). Mechanism and consequences for paralogspecific
sumoylation of ubiquitin-specific protease 25. Mol. Cell
30, 610-669.
Mossessova, E. and Lima, C. D. (2000). Ulp1-SUMO crystal
structure and genetic analysis reveal conserved interactions and a
regulatory element essential for cell growth in yeast. Mol. Cell 5,
865-876.
Mukhopadhyay, D. and Dasso, M. (2007). Modification in
reverse: the SUMO proteases. Trends Biochem. Sci. 32, 286-295.
Mukhopadhyay, D., Ayaydin, F., Kolli, N., Tan, S. H., Anan,
T., Kametaka, A., Azuma, Y., Wilkinson, K. D. and Dasso, M.
(2006). SUSP1 antagonizes formation of highly SUMO2/3conjugated
species. J. Cell Biol. 174, 939-949.
Ouyang, J., Shi, Y., Valin, A., Xuan, Y. and Gill, G. (2009).
Direct binding of CoREST1 to SUMO-2/3 contributes to genespecific
repression by the LSD1/CoREST1/HDAC complex.
Mol. Cell 34, 145-154.
Palvimo, J. J. (2007). PIAS proteins as regulators of small
ubiquitin-related modifier (SUMO) modifications and
transcription. Biochem. Soc. Trans. 35, 1405-1408.
Panse, V. G., Kressler, D., Pauli, A., Petfalski, E., Gnadig, M.,
Tollervey, D. and Hurt, E. (2006). Formation and nuclear export
of preribosomes are functionally linked to the small-ubiquitinrelated
modifier pathway. Traffic 7, 1311-1321.
Peng, J. and Wysocka, J. (2008). It takes a PHD to SUMO.
Trends Biochem. Sci. 33, 191-194.
Pichler, A., Gast, A., Seeler, J. S., Dejean, A. and Melchior, F.
(2002). The nucleoporin RanBP2 has SUMO1 E3 ligase activity.
Cell 108, 109-120.
Pickart, C. M. and Fushman, D. (2004). Polyubiquitin chains:
polymeric protein signals. Curr. Opin. Chem. Biol. 8, 610-616.
Potts, P. R. (2009). The Yin and Yang of the MMS21-SMC5/6
SUMO ligase complex in homologous recombination. DNA
Repair (Amst) 8, 499-506.
Reverter, D. and Lima, C. D. (2004). A basis for SUMO
protease specificity provided by analysis of human Senp2 and a
Senp2-SUMO complex. Structure 12, 1519-1531.
Reverter, D. and Lima, C. D. (2005). Insights into E3 ligase
activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.
Nature 435, 687-692.
Reverter, D. and Lima, C. D. (2006). Structural basis for SENP2
protease interactions with SUMO precursors and conjugated
substrates. Nat. Struct. Mol. Biol. 13, 1060-1068.
Saitoh, H. and Hinchey, J. (2000). Functional heterogeneity of
small ubiquitin-related protein modifiers SUMO-1 versus
SUMO-2/3. J. Biol. Chem. 275, 6252-6258.
Saitoh, H., Sparrow, D. B., Shiomi, T., Pu, R. T., Nishimoto,
T., Mohun, T. J. and Dasso, M. (1998). Ubc9p and the
conjugation of SUMO-1 to RanGAP1 and RanBP2. Curr. Biol.
8, 121-124.
Shen, L., Tatham, M. H., Dong, C., Zagorska, A., Naismith,
J. H. and Hay, R. T. (2006a). SUMO protease SENP1 induces
isomerization of the scissile peptide bond. Nat. Struct. Mol. Biol.
13, 1069-1077.
Shen, L. N., Dong, C., Liu, H., Naismith, J. H. and Hay, R. T.
(2006b). The structure of SENP1-SUMO-2 complex suggests a
structural basis for discrimination between SUMO paralogues
during processing. Biochem. J. 397, 279-288.
Shen, L. N., Geoffroy, M. C., Jaffray, E. G. and Hay, R. T.
(2009). Characterization of SENP7, a SUMO-2/-3 specific
isopeptidase. Biochem. J. 2, 223-230.
Sun, H., Leverson, J. D. and Hunter, T. (2007). Conserved
function of RNF4 family proteins in eukaryotes: targeting a
ubiquitin ligase to SUMOylated proteins. EMBO J. 26, 4102-
4112.
Takahashi, Y., Kahyo, T., Toh, E. A., Yasuda, H. and Kikuchi,
Y. (2001). Yeast Ull1/Siz1 is a novel SUMO1/Smt3 ligase for
septin components and functions as an adaptor between
conjugating enzyme and substrates. J. Biol. Chem. 276, 48973-
48977.
Tatham, M. H., Jaffray, E., Vaughan, O. A., Desterro, J. M.,
Botting, C. H., Naismith, J. H. and Hay, R. T. (2001).
Polymeric chains of SUMO-2 and SUMO-3 are conjugated to
protein substrates by SAE1/SAE2 and Ubc9. J. Biol. Chem. 276,
35368-35374.
Vertegaal, A. C., Andersen, J. S., Ogg, S. C., Hay, R. T., Mann,
M. and Lamond, A. I. (2006). Distinct and overlapping sets of
SUMO-1 and SUMO-2 target proteins revealed by quantitative
proteomics. Mol. Cell Proteomics 5, 2298-2310.
Weger, S., Hammer, E. and Heilbronn, R. (2005). Topors acts
as a SUMO-1 E3 ligase for p53 in vitro and in vivo. FEBS Lett.
579, 5007-5012.
Wotton, D. and Merrill, J. C. (2007). Pc2 and SUMOylation.
Biochem. Soc. Trans. 35, 1401-1404.
Yang, X. J. and Gregoire, S. (2006). A recurrent phosphosumoyl
switch in transcriptional repression and beyond. Mol. Cell
23, 779-786.
Yun, C., Wang, Y., Mukhopadhyay, D., Backlund, P., Kolli,
N., Yergey, A., Wilkinson, K. D. and Dasso, M. (2008).
Nucleolar protein B23/nucleophosmin regulates the vertebrate
SUMO pathway through SENP3 and SENP5 proteases. J. Cell
Biol. 183, 589-595.
Yunus, A. A. and Lima, C. D. (2006). Lysine activation and
functional analysis of E2-mediated conjugation in the SUMO
pathway. Nat. Struct. Mol. Biol. 13, 491-499.
Yunus, A. A. and Lima, C. D. (2009). Structure of the Siz/PIAS
SUMO E3 ligase Siz1 and determinants required for SUMO
modification of PCNA. Mol. Cell 35, 669-682.
Zeng, L., Yap, K. L., Ivanov, A. V., Wang, X., Mujtaba, S.,
Plotnikova, O., Rauscher, F. J., 3rd. and Zhou, M. M.
(2008). Structural insights into human KAP1 PHD fingerbromodomain
and its role in gene silencing. Nat. Struct. Mol. Biol.
15, 626-633.
Zhang, X. D., Goeres, J., Zhang, H., Yen, T. J., Porter, A. C.
and Matunis, M. J. (2008). SUMO-2/3 modification and binding
regulate the association of CENP-E with kinetochores and
progression through mitosis. Mol. Cell 29, 729-741.
Zhao, X., Sternsdorf, T., Bolger, T. A., Evans, R. M. and Yao,
T. P. (2005). Regulation of MEF2 by histone deacetylase 4- and
SIRT1 deacetylase-mediated lysine modifications. Mol. Cell.
Biol. 25, 8456-8464.
Zhu, J., Zhu, S., Guzzo, C. M., Ellis, N. A., Sung, K. S., Choi,
C. Y. and Matunis, M. J. (2008). Small ubiquitin-related
modifier (SUMO) binding determines substrate recognition and
paralog-selective SUMO modification. J. Biol. Chem. 283,
29405-29415.
Zhu, S., Goeres, J., Sixt, K. M., Bekes, M., Zhang, X. D.,
Salvesen, G. S. and Matunis, M. J. (2009). Protection from
isopeptidase-mediated deconjugation regulates paralog-selective
sumoylation of RanGAP1. Mol. Cell 33, 570-580.
Cell Science at a Glance on the Web
Electronic copies of the poster insert are available
in the online version of this article at
jcs.biologists.org. The JPEG images can be
downloaded for printing or used as slides.