Download how the ubiquitin–proteasome system controls transcription

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HOW THE UBIQUITIN–PROTEASOME
SYSTEM CONTROLS TRANSCRIPTION
Masafumi Muratani*‡ and William P. Tansey*
Gene transcription and ubiquitin-mediated proteolysis are two processes that have seemingly
nothing in common: transcription is the first step in the life of any protein and proteolysis the
last. Despite the disparate nature of these processes, a growing body of evidence indicates
that ubiquitin and the proteasome are intimately involved in gene control. Here, we discuss the
deep mechanistic connections between transcription and the ubiquitin–proteasome system,
and highlight how the intersection of these processes tightly controls expression of the genetic
information.
GENERAL TRANSCRIPTION
FACTORS
A broadly expressed set of
proteins that are generally
required for accurate, promoterinitiated, transcription by RNA
polymerase II.
UBIQUITIN
A highly-conserved
76-amino-acid protein that is
linked covalently to lysine
residues in other proteins and
often signals their destruction.
PROTEASOME
A large, self-compartmentalized
protease complex that destroys
ubiquitylated substrates. The
entire proteasome is often
referred to as the 26S complex,
which can be separated further
into a 20S catalytic and a 19S
regulatory complex.
*Cold Spring Harbor
Laboratory and
‡
Watson School of Biological
Sciences, 1 Bungtown Road,
PO Box 100,
Cold Spring Harbor,
New York 11724, USA.
Correspondence to W. P. T.
e-mail: [email protected]
doi:10.1038/nrm1049
The correct regulation of gene expression is a demanding but vitally important process. As most eukaryotic
cells carry an entire organism’s worth of genetic information, controlling which genes are turned on, and
when, is essential for normal growth and development.
It is not surprising, therefore, that cells have evolved
elaborate mechanisms to regulate the first step in gene
expression — transcription (BOX 1). The complex interplay between transcriptional regulators, GENERAL
TRANSCRIPTION FACTORS and chromatin structure establishes a barrier to gene activation, which ensures that
genes are transcribed only when appropriate signals
make their way to the nucleus.
But it takes more than just an elaborate series of
interactions to control transcription accurately. The
transcription proteins themselves have to be present
at the right place, at the right time and in the correct
amounts, and their activity has to be fine-tuned to
produce levels of transcription that are appropriate
for each gene. In recent years it has become evident
that one of the ways in which cells meet this regulatory challenge is to make extensive use of the UBIQUITIN
(Ub)–PROTEASOME system (BOX 2). Although this system
first came to light in the context of protein destruction1, it is now clear that both ubiquitin and the proteasome can also carry out various non-proteolytic
tasks, controlling activities as diverse as receptor
internalization2, ribosome function3 and nucleotide
excision repair4. The impressive range of activities
carried out by the Ub–proteasome system makes it
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ideally suited to controlling the distribution, abundance and activity of components of the transcriptional machinery.
In this review, we discuss how Ub, Ub-like proteins
(BOX 2) and the proteasome regulate gene expression. We
describe how both the proteolytic and non-proteolytic
activities of this system modulate transcription at different levels, and review evidence that points to an
extensive and intimate interconnection between transcription and the Ub–proteasome system. The marriage
of these two cellular processes, although recognized
only recently, is likely to reflect an ancient connection
with profound consequences for the regulation of gene
expression.
Ubiquitin and chromatin
The role of the Ub–proteasome system in transcription
has generated much excitement recently, largely because
it is a previously unrecognized level of transcriptional
control. It should be noted, however, that the involvement of Ub in transcription is nothing new — conspicuous hints of connections between the two processes
have been made in the past several decades. Nowhere is
this better illustrated than by the involvement of Ub in
the regulation of chromatin. It is worth remembering
that the first ubiquitylated protein to be described was
histone H2A, as investigators characterized a variant
histone, A24, the levels of which changed in response to
certain stimuli5–7. Later, studies in Drosophila8,
Tetrahymena9–12 and mammalian cells13 showed that the
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Box 1 | Transcriptional control
Co-activators
General transcription
factors
HAT
Activator
Ac
Ac
Ac
Nucleosome
Repressor
HDAC
Co-repressors
The regulation of gene transcription is controlled both positively and negatively by
transcriptional activators and repressors, respectively (see figure). Both types of
control proteins are typically modular, with a DNA-binding domain that tethers them
to promoter DNA and a functional domain that is responsible for activation or
repression. Activators function through numerous mechanisms: first, the recruitment
of histone-modifying and -remodelling activities, such as histone acetyl transferases
(HATs); second, direct contact with components of the general transcription
machinery, including TATA-binding protein (TBP), TFIIB and TFIIH, and RNA
polymerase itself; and third, the interaction with transcriptional co-activators that
facilitate activation in response to one activator, but not another. The net effect of
these interactions is to reconfigure the chromatin at the locus, recruit RNA
polymerase to the 5′ end of the gene’s coding sequence and transcribe the gene. Some
activators preferentially regulate one or more steps — glutamine-rich activators, for
example, stimulate the initiation of transcription, whereas acidic activators can
stimulate both the initiation and elongation of transcription94. Not surprisingly,
transcriptional repressors antagonize many of the same steps; the deacetylating of
histones by histone deacetylase (HDAC), blocking the recruitment of the general
transcription machinery and interacting with transcriptional co-repressors.
UBIQUITYLATION
The process whereby ubiquitin is
conjugated to a substrate
protein. This is the chemicallyappropriate terminology, as
opposed to ‘ubiquitination’ and
‘ubiquitinylation’.
UBIQUITIN-CONJUGATING
ENZYME.
(Ubc). The enzyme that is
responsible for catalysing the
transfer of ubiquitin to substrate
proteins, and which might or
might not be involved directly in
substrate recognition.
TELOMERIC-GENE SILENCING
The transcriptional
downregulation (silencing) of
the expression of genes that are
proximal to the telomere.
2
ubiquitylated forms of histones H2A and H2B were
associated specifically with actively transcribed genes,
making histone UBIQUITYLATION one of the first markers of
transcriptionally active chromatin to be recognized.
Together with H2A and H2B, ubiquitylated forms of
histones H1 (REF. 14) and H3 (REF. 15) have since been
reported in studies of various eukaryotic species.
Despite the well-established connection between histone ubiquitylation and transcription, only recently
have the underlying mechanisms begun to emerge (FIG. 1).
The best-understood example of how histone ubiquitylation regulates transcription comes from the yeast
Saccharomyces cerevisiae, in which monoubiquitylation
of histone H2B — mediated by the UBIQUITIN-CONJUGATING
ENZYME (Ubc) Rad6 (REF. 16) — is implicated in both
transcriptional repression of the argininosuccinate
synthase gene ARG1 (REFS 17,18) and the maintenance of
19,20
TELOMERIC-GENE SILENCING
. In both cases, H2B ubiquitylation influences other chromatin modifications, such as
acetylation17,18,21 and methylation22,23, to control transcription. Indeed, the ubiquitylation of H2B (uH2B) is
required for methylation of another histone, H3, at
lysine residues 4 (K4) and 79 (K79)22,23 — histone H3
methylation, in turn, is required for telomeric-gene
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silencing24. The interplay between uH2B and methyl-H3
establishes the mechanism through which uH2B contributes to gene silencing, and indicates that histone
ubiquitylation is an integral part of the HISTONE CODE25
that cells use to distinguish transcriptionally active from
inactive chromatin.
But how does ubiquitylation regulate other histone
modifications, and why does the cell use a bulky Ub
moiety, when profound regulatory changes can be
achieved with phosphorylation, acetylation and methylation events? The received wisdom is that histone ubiquitylation is generally not associated with histone
destruction, although several studies have indicated that
histone metabolism is highly dynamic, even in nondividing cells26–28. It is difficult to argue, however, for a
proteolytic role for this modification, because highly
multi-ubiquitylated histones have not been described,
and because it is unclear just how many histones at any
given locus are ubiquitylated. It seems more probable
that histone ubiquitylation has a structural role, either
directly (perhaps by ‘loosening’ chromatin structure) or
indirectly (perhaps by recruiting factors such as the proteasome29 and histone deacetylase 6 (REF. 30), both of
which have Ub-binding abilities).
From all of the evidence, it seems as though the
involvement of uH2B in transcriptional silencing is only
the tip of a much larger iceberg. As histone H3 methylation is also a mark of transcriptionally active genes31, it is
likely that uH2B also participates in gene activation, at
least at some promoters. Moreover, the TATA-binding
protein (TBP)-associated factor TAFII250, which forms
a scaffold for the assembly of the general transcription
factor TFIID complex32, ubiquitylates specifically the
linker histone H1 (REF. 14), a function that might well be
related to its role as a transcriptional co-activator. And,
finally, histone DE-UBIQUITYLATION is also looming on the
horizon as an important transcription-regulatory
process, on the basis of studies that have identified Ubspecific proteases (Ubps) that are associated with components of both the SIR4 silencing33 and the
Spt–Ada–Gcn5–acetyltransferase (SAGA) chromatinremodelling complexes34. Undoubtedly, as more of the
relevant UBIQUITIN LIGASES and de-ubiquitylating enzymes
are discovered, the full extent to which histone ubiquitylation features in gene control will be revealed.
Regulating RNA polymerase
The ultimate goal of any transcriptional control process
is to govern the recruitment and activity of RNA polymerase II (pol II). Unless pol II can initiate transcription
at the 5′ end of a gene and successfully transcribe the
complete message, a protein product cannot be produced. Not surprisingly, therefore, pol II is itself a target
for regulation, including regulation by ubiquitylation.
At present, although our understanding of this process
is focused on regulating pol II during transcriptioncoupled repair (TCR), there are indications that ubiquitylation of pol II might have a more general role in
transcriptional control.
When eukaryotic cells are exposed to DNA-damaging agents, one of their first priorities is to repair
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Box 2 | Ubiquitin-family proteins and the proteasome
The ubiquitin (Ub) system defines a family of related
Ub
Ub-family members
modifier proteins that are linked covalently to target
Ubiquitin
proteins. Ubiquitin is the defining member of this class, but
SUMO-1, -2, -3
Ubc (E2)
at least nine other related proteins with this function have
NEDD8
HUB
been described (see figure). Ubiquitylation is a specific
Ub
Ubl (E3)
ISG15
process that is signalled by an element — a degradation
Degron
K
APG-8, -12
signal (degron) — in the substrate protein. The degron is
URM1
recognized by a Ub-ligase (Ubl), E3, which in turn recruits a
Ub
Ub-conjugating (Ubc) enzyme, E2, to the substrate. The E3
Ub
Ub
then catalyses the transfer of Ub groups to a lysine (K)
Ub
residue that is somewhere in the target protein. The exact
Degron
nature of ubiquitylation determines the fate of the substrate
protein. If a multi-Ub chain — linked by lysine 48 (K48) in
Ub itself — forms, the substrate is targeted for destruction by
Lid
19S regulatory complex
a large, self-compartmentalized, protease known as the 26S
Base
proteasome. The 19S subcomplex of the proteasome
recognizes the multi-ubiquitylated substrate, removes the Ub
20S protease complex
groups, unfolds the substrate and feeds it into the core of the
20S subcomplex where it is destroyed. If, however, the multiUb chain is linked by lysine 63 (K63), or if it has less than
four Ub chains, proteolysis does not occur (not shown). The other Ub-family members are similarly conjugated to lysine
residues on substrates by dedicated E2 and E3 enzymes, but they usually regulate function without signalling
proteasomal destruction. HUB, homologous to ubiquitin; ISG15, interferon-stimulated gene 15; NEDD8, neural
precursor cell-expressed developmentally downregulated 8; SUMO, small ubiquitin-related modifier; URM1, ubiquitinrelated modifier 1.
HISTONE CODE
The pattern of covalent
modifications on core histones
that functions as an epigenetic
mark that distinguishes
transcriptionally active regions
from inactive regions of the
genome.
DE-UBIQUITYLATION
The removal of ubiquitin by
cleavage of the isopeptide bond
that links ubiquitin to the
substrate protein.
UBIQUITIN LIGASE
(Ub-ligase). A substrate
recognition factor that brings a
ubiquitin-conjugating enzyme
and the substrate together. It is
often a multiprotein complex.
TCR
(Transcriptional-coupled
repair). The process by which
transcriptionally active genes are
preferentially repaired following
DNA damage.
transcriptionally active genes 35. This mandate is
achieved, in part, when active pol II — having stalled
at a DNA lesion — is ubiquitylated and presumably
destroyed by the proteasome (FIG. 2; REFS 36–38).
The removal of pol II is then followed by the coordinated recruitment of the DNA-repair machinery, and
repair of the damaged DNA. In this way, cells are able
to use pol II to probe for DNA damage and shut
down expression of the genetic information until
damaged DNA segments are corrected.
The success of TCR as a protective strategy depends
on the ability of Ub-ligases to recognize transcriptionally active, but stalled, RNA polymerase molecules. One
way this is probably achieved is through phosphorylation events in the carboxy-terminal domain (CTD) of
the largest subunit of pol II. The phosphorylation status of the pol II CTD changes during transcription39,
and it has been suggested that CTD phosphorylation
functions as a kind of molecular beacon that signals the
unique transcriptional status of elongating RNA polymerase molecules. Given that CTD phosphorylation
promotes pol II ubiquitylation37,40, it is reasonable to
speculate that a specific pattern of CTD phosphorylation shown by a stalled polymerase functions as a direct
signal for ubiquitylation.
Despite recent advances in our understanding of this
process, however, there are many important questions
that remain unanswered. For example, is ubiquitylation
of pol II just signalling its destruction, or is there another
function for this modification in TCR? Does pol II ubiquitylation facilitate the disengagement of this otherwise
processive enzyme from its template? Or does ubiquitylation function to recruit components of the DNA-repair
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machinery? Moreover, it is not known if pol II ubiquitylation occurs only in times of crisis, or if there is also a
function for this modification in unstressed cells.
Curiously, Rsp5, the putative Ub-ligase for pol II (REF. 38),
is a co-activator for the steroid-hormone receptor family
of transcription factors41, and Def1 — a component of
the Rad26 TCR DNA-repair complex — has recently
been shown to have an essential function in normal
Rad6
Silencing
Me
Ub
H2B (K123) H3 (K4,K79)
H1
Nucleosome
H1
Ub
General
transcription
factors
TAFII250
?
Figure 1 | Control of chromatin by ubiquitin. The ubiquitin
(Ub)-conjugating enzyme Rad6 ubiquitylates lysine 123
(K123) in the core of histone H2B. Through an unknown
mechanism, this modification promotes the methylation of
another histone, H3, at two positions, lysine 4 (K4) and lysine
79 (K79). These H3 modifications, in turn, are required for
telomeric-gene silencing. Although depicted as
internucleosomal regulation, it is not known whether these
modifications occur on the same nucleosome, or indeed
whether each H2B molecule at a locus is ubiquitylated. In
addition, TAFII250, which is a component of the general
transcription factor TFIID, can ubiquitylate the linker histone
H1; the significance of this ubiquitylation is unknown, but it
might relate to the role of this TATA-binding protein (TBP)associated factor (TAF) in transcriptional activation.
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a
RNA
pol II
DNA
P
P
b
pol II
P
P
P
P
P
c
pol II
Ub Ub
Rsp5
DNA-repair
machinery
Ub
Ub Ub
Ub
d
DNA-repair
machinery
Figure 2 | Regulation of TCR by ubiquitylation of RNA
polymerase II. Transcription-coupled repair (TCR) is the
mechanism through which mutations in actively transcribed
genes are preferentially repaired. a | Elongating RNA polymerase
II (pol II), which has a unique pattern of phosphorylation on its
carboxy-terminal domain (CTD), encounters a damaged DNA
segment. The stalled polymerase (b) then recruits the ubiquitin
(Ub)-ligase Rsp5 (c), which in turn ubiquitylates the largest
subunit of pol II in a CTD-phosphorylation-dependent manner.
d | Ubiquitylation is followed by the proteasomal destruction of at
least one subunit of polymerase, recruitment of the repair
machinery and restoration of DNA integrity.
transcriptional elongation42. It might be, therefore, that
components of the TCR response — including pol II
ubiquitylation — have an integral role in regulating
elongation of transcription by this enzyme.
Regulating the regulators
SUMO
(small ubiquitin-related
modifier). One of a family of
small ubiquitin-related proteins
that are conjugated to substrates
in a manner that is analogous to
ubiquitylation.
4
Most of our understanding of how the Ub–proteasome
system impacts on transcription is focused on transcriptional activators. Part of this focus on activators is
undoubtedly due to their tractability, but part is also
attributable to their principal role in determining when
and where any particular gene will be transcribed.
Although there is a wealth of literature that details the
complex regulation of activators by the Ub–proteasome
system, the fundamental mechanisms boil down to just
three functions — the regulation of activator location,
activity and abundance (FIG. 3).
Controlling activator location. It is obvious that if a
transcription factor is not in the nucleus, it cannot activate transcription. This simple mechanism of regulation
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is used extensively to control gene expression, and is
achieved by phosphorylation43, site-specific proteases44
and by the judicious use of the Ub–proteasome system.
The most straightforward example from the latter category is that of nuclear factor (NF)-κB, which is held in
the cytoplasm by interaction with the inhibitor protein
IκB. During inflammation, IκB is phosphorylated,
ubiquitylated and destroyed by the proteasome45, which
allows NF-κB to drift into the nucleus. A similar, but
more elaborate, mechanism is used to regulate the location of the yeast transcriptional activator Spt23, which
controls the synthesis of genes that are required for
fatty-acid metabolism46. Intriguingly, Spt23 is synthesized as a precursor that sits in the outer membrane of
the endoplasmic reticulum (ER). When fatty-acid levels
in the ER membrane drop, Spt23 is ubiquitylated,
clipped from its membrane tether by the proteasome
and escorted from the ER by a Ub-specific chaperone47.
Spt23 — possibly still carrying its Ub tags — then
enters the nucleus where, like NF-κB, it activates appropriate target genes. In both cases, by engaging the
Ub–proteasome system, cells elicit an efficient and irreversible transcriptional response to a signal that is
sensed outside the nucleus.
Simply entering the nucleus, however, does not guarantee that a transcription factor will be able to access its
target genes. The internal organization of the nucleus
can regulate gene expression, and in this regard it is
interesting to note that our understanding of subnuclear
transcription-factor domains has evolved in parallel
with that of a Ub-family member, SUMO. When observed
by indirect immunofluorescence, many transcription
factors seem to congregate in discrete nuclear domains,
such as those that were first reported for the promyelocytic leukaemia (PML)–retinoic acid receptor (RAR)
fusion protein48. These nuclear bodies are enriched in
SUMO49, and in several cases, SUMOylation of activators correlates with their entry into nuclear bodies.
Although the functional consequences of SUMOylation
and nuclear-body formation have not always been clear,
a growing body of evidence supports a role in transcriptional repression. For example, the SUMO-ligase PIASy
SUMOylates the transcriptional activator Lef1, which
causes both nuclear-body localization and attenuation
of Lef1 transcriptional activity50. Similar mechanisms
have been reported for Sp3 (REFS 51,52), Myb53, the androgen receptor54, p53 (REF. 55), Jun55 and C/EBP56. Together,
these cases support a model in which SUMOylation
sequesters activators into specific nuclear domains,
physically disconnecting them from the remainder of
the nucleoplasm.
Controlling activator activity. Apart from the direct
effects on activator location and stability, ubiquitylation
can influence transcription by regulating the association
of transcription factors with partner proteins that are
required for activation of certain genes. The Ub-ligase
RLIM, for example, recognizes a DNA-bound complex
of the transcription factor LIM and its co-activator,
CLIM, and specifically targets CLIM for Ub-mediated
destruction57. In this way, destruction of the co-activator,
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a
Nuclear body
b
S
Ub
Ub
Ub
Co-activator A
Nucleus
c
Co-activator B
Nucleus
d
Ub
Signal
General
transcription
factors
Default
Ub
26S
proteasome
Nucleus
Nucleus
Figure 3 | Regulation of activators by the ubiquitin–proteasome system. The ubiquitin
(Ub)–proteasome system controls the localization, abundance and activity of transcriptional
activators (red ellipse). a | Regulating location. As with nuclear factor (NF)-κB, the transcription
factor can be maintained outside the nucleus by interactions with an inhibitor (IκB) that is
destroyed by the Ub–proteasome system. In addition, the Ub-family member SUMO (S) can
directly ubiquitylate activators and sequester them into nuclear bodies. b | Regulating activity.
Ubiquitylation can regulate the association of activators with co-activator proteins either directly,
by blocking the association of an activator with its essential cofactor, or indirectly, by facilitating
the exchange of cofactors with an activator. c | Regulating abundance I — constitutive turnover.
By maintaining an activator in a constitutively unstable form, cells are primed for a transcriptional
response when appropriate. In this model, a signal from outside the nucleus leads to a transient
stabilization of the activator, which elicits a rapid induction of target genes.
d | Regulating abundance II — transcription-coupled destruction. In this model, activators are
destroyed during the act of transcriptional activation as a way of limiting uncontrolled activation
by any one DNA-bound transcription factor. It should be noted that this model is not mutually
exclusive with that presented in c, and that the two mechanisms might work together.
TRANSCRIPTIONAL ACTIVATION
DOMAIN
(TAD). A region in a
transcription factor that
interacts with the general
transcriptional machinery to
stimulate transcription.
DEGRON
(degradation signal). A specific
element in a target protein that
signals proteolysis. Usually the
site of interaction with a
ubiquitin ligase, but not
necessarily the site of ubiquitin
attachment.
and not the promoter-bound LIM, allows for a new coactivator to enter the promoter complex, reprogramming the transcriptional response. In a similarly effective
method, the Ub-ligase SCFMet30 has been shown to oligoubiquitylate the transcription factor Met4 and block its
transcriptional activity by hindering the recruitment of a
transcriptional partner protein58. There is debate as to
whether SCFMet30 also signals the destruction of Met4
(REF. 59), or whether this is strictly regulation of Met4 activity without proteolysis58, but it has recently been reported
that the switch between Ub-mediated Met4 inactivation
versus Met4 destruction is controlled by nutrients60.
Although the significance of this switching is unclear, it
does give a glimpse of the subtle levels of regulation that
can be achieved by putting the Ub–proteasome system to
work in this context.
Controlling activator levels. One of the things that the
Ub–proteasome system does best is destroy proteins, and
transcription factors do not escape this ultimate level of
regulation. Most interesting about transcription-factor
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destruction, however, are the unique strategies that cells
have evolved to control activator abundance by using
this system. One strategy has been to take the approach
that is used in cell-cycle regulation, of destroying proteins when they are no longer needed, and then to run
the Ub–proteasome system in reverse — shutting off
proteolysis when a rapid transcriptional response is
required. This type of regulation is perhaps best illustrated by β-catenin, a principal player in the Wnt signalling pathway61. In the absence of Wnt signalling,
β-catenin is phosphorylated by glycogen synthase
kinase-3β (GSK-3β), which in turn signals for β-catenin
ubiquitylation and then its efficient destruction by
the proteasome62. The binding of Wnt to its cell-surface receptor inactivates GSK-3β, rapidly stabilizing
β-catenin63, and allowing the efficient activation of
downstream target genes. By using Ub-mediated proteolysis to destroy β-catenin in this way, cells establish a
low baseline of β-catenin activity, while at the same time
remaining primed and ready to respond to the Wnt signal when it arrives. Similar strategies are used by p53
(REF. 64) and hypoxia-inducible factor (HIF)-1α (REF. 65).
Another proteolytic strategy, which so far seems to
be restricted to transcription control, is to couple the
activity of transcription factors tightly to their proteolytic destruction. This phenomenon of ‘unstable when
active’ — which is seen with many transcription factors
(for example, the aryl hydrocarbon receptor66, SMAD2
(REF. 67), STATs68) — allows tight control over transcription, by ensuring that the activation of any gene is
linked to the ongoing synthesis of its transcriptional
regulator.
But how does a cell detect when a transcription factor is active, and how are the events of gene activation
and activator destruction coupled? Although there are
no definitive answers to these questions as yet, a growing body of evidence indicates that mechanisms for
marking and destroying active transcription factors are
integrated into the activation process itself. One compelling piece of evidence in this regard is the functional
relationship between TRANSCRIPTIONAL ACTIVATION DOMAINS
(TADs) and degradation signals (DEGRONS). In almost
all unstable transcription factors that have been characterized — in eukaryotes as well as eubacteria69,70 —
there is an overlap between TAD and degron
sequences (FIG. 4). In addition, studies of natural71 and
synthetic72,73 activation domains have shown that there
is an intimate connection between the ability of a TAD
to activate transcription and to signal proteolysis. The
distinction between TADs and degrons is blurred further by the observation that degrons isolated from yeast
cyclins can activate transcription72. The simplest interpretation of these experiments is that activation
domains and some degrons are functionally equivalent,
which implies that there is a coupled mode of action
for each element. Moreover, the existence of this relationship in eubacteria — which lack a Ub–proteasome
system — indicates that the coupling of transcriptionfactor activity and destruction is a fundamentally
important, and evolutionarily conserved, cellular
process.
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σ32
DBD
σs
DBD
ATF6 TAD
DBD
DBD
TAD
E2F-1
TAD
DBD
TAD
ERα
TAD
TAD
DBD
Fos
TAD
DBD GCN4
TAD
TAD
GR
DBD
DBD
TAD
DBD
TAD
DBD
DBD Jun
MITF
TAD
TAD
DBD
DBD
DBD
DBD
TAD
Degron
p53
DBD
RARγ
TAD
TAD
DBD
Myc
TAD Myf5
TAD
TAD
HIF1-α
IRF-1
TAD
TAD
AD
E2 (HPV)
DBD
DNA-binding domain
Transcriptional
activation domain
Rel
Degron
STAT5
DBD
TAD
Figure 4 | TADs and degrons overlap. The transcriptional activation domains (TADs) and
degradation signals (degrons) overlap 19 unstable transcription factors. It should be noted that
σ32 and σS are eubacterial activators; because there is no ubiquitin (Ub)–proteasome system in
eubacteria, the term ‘degron’ applies to an element that signals protein destruction, rather than
ubiquitylation. The MITF and Myf5 degrons have not been mapped extensively — what is
indicated in these cases is the position of phosphorylation sites that are essential for Ubmediated turnover. ATF6, activating transcription factor 6; E2F-1, E2 promoter binding factor-1;
E2 (HPV), E2, human papillomavirus; GR, glucocorticoid receptor; HIF-1α, hypoxia-inducible
factor 1α; IRF-1, interferon regulatory factor-1; MITF, microphthalmia-associated transcription
factor; Myf5, myogenic factor 5; RARγ, retinoic acid receptor γ; STAT5, signal transducer and
activator of transcription 5.
One way that this coupling could be achieved is
by the coordinated action of the ubiquitylation and
transcription machineries. The recent discovery that
Ub-ligase activity associates with RNA polymerase74 is
consistent with this idea (see below), as is the regulation
of GCN4 by Srb10 (REF. 75). GCN4, which is a yeast activator that is involved in amino-acid biosynthesis, is targeted for ubiquitylation in a manner that is dependent
on Srb10-mediated phosphorylation. This is intriguing,
because Srb10 is a component of the pol II
holoenzyme76, which implies that Srb10 and GCN4 meet
during the activation process. The ability of the basal
transcription machinery to mark an activator for
destruction has led to a ‘black widow’77 or ‘kamikaze’78
model for activation, in which simply activating transcription is the signal for activator turnover.
A striking twist in this model has come from the
analysis of the role of a Ub-ligase in transcriptional activation. In yeast, activators that bear the prototypical
VP16 activation domain are targeted for Ub-mediated
proteolysis by an SCFMet30 Ub-ligase complex79.
Disruption of the substrate-binding component of this
6
ligase, Met30, not only blocks the degron function of the
VP16 TAD, but also blocks its ability to activate transcription. This transcriptional defect can be rescued by
the direct fusion of Ub to the VP16 activator, which
shows that activator ubiquitylation is required for transcriptional activity. The requirement for ubiquitylation
indicates that engagement of the Ub–proteasome system by activators is part of their modus operandi, and
functions to ‘license’ transcription-factor activity, by
inexorably linking the activity of a transcription factor
to its destruction by the proteasome.
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Common components — a smoking gun?
Scientists take great comfort in classifying proteins
according to function: it is natural to assume that a protein involved in DNA replication, for example, will not
be involved in pre-messenger RNA splicing. The close
functional relationship between transcription and
ubiquitin-mediated proteolysis, however, predicts that
our classification of what is a transcription factor and
what is a component of the Ub–proteasome system
must be broken down. Although this area is still in its
infancy, there are several proteins (TABLE 1) that defy a
singular classification and seem to have a role in both
transcription and Ub–proteasome function.
The most conspicuous example of a functionally
‘cross-dressing’ factor is the proteasome itself. Indeed,
one subunit of the proteasome, Sug1 (which is also
known as Rpt6)80, made its debut as a transcriptional
regulator. Sug1 is one of six AAA-type ATPases that
are in the base of the 19S regulatory complex81, and
was identified by genetic interactions with the yeast
activator Gal4 (REF. 82). Johnston and colleagues isolated recessive mutations in the gene encoding Sug1
— and later another 19S component, Sug2 (which is
also known as Rpt4; REF. 83) — that could suppress the
effects of deleting the Gal4 TAD, which indicates that
Sug1 might be a transcriptional target for Gal4. This
idea was supported further by biochemical data that
showed that Sug1 could interact with the Gal4 TAD84
— and several other TADs85–87 — as well as with the
general transcription factors TBP88,89 and TFIIH 90.
Sug1 was also found in some preparations of the pol
II holoenzyme 91, although it is unlikely that Sug1
associates with the pol II holoenzyme in a stable and
stoichiometric way, as it does with the proteasome.
So how do Sug1 and Sug2 participate in transcription? As mutations in 20S components of the proteasome do not suppress deletions of the Gal4 TAD92, it has
been argued that the role of these Sug proteins is distinct
from proteolysis. Instead, it seems as though Sug1 and
Sug2, and probably other components of the 19S complex, participate directly in transcription, most probably
during the elongation phase. Sug mutants confer sensitivity to 6-azauracil93 — a hallmark of elongation
defects — and the 19S subunit of the proteasome is
required for efficient transcriptional elongation in
vitro93. In this regard, it is most curious that the TADs
that signal proteolysis — those rich in acidic residues72
— are those that also signal efficient transcriptional
elongation94, because it indicates that there might be a
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Table 1 | Potentially common components of the transcription and the ubiquitin–proteasome systems
Component
Roles in transcription and the Ub–proteasome system
CCR4–Not
Transcriptional repressor complex, contains a Ub-ligase
References
98
Elongin B, Elongin C
Components of a Ub-ligase complex that associates with the pol II holoenzyme through Med8
First isolated as factors that stimulate transcriptional elongation
74
99
Med8
Component of the pol II ‘mediator’ complex
Associates with affinity-purified 26S proteasomes
Associates with the mammalian Elongin B–C complex
96
95
74
Paf1, Leo1, Ctr9
Form a complex that associates with pol II and has an important role in transcriptional elongation
Associates with affinity-purified 26S proteasomes
100
95
Rsp5
Ub-conjugating enzyme
Interacts with the pol II CTD
Ubiquitylates pol II in TCR
Co-activator for steroid-hormone receptors
101
38
37
41
Sug1, Sug2
AAA ATPases in the base of 19S complex
Associate with the pol II holoenzyme
Isolated as suppressors of mutations in Gal4 TAD
TAFII250
Core-component of the TFIID complex
Ub-ligase for histone H1
Tom1
Transcriptional co-activator and component of the SAGA chromatin-remodelling complex, and
Ub-conjugating enzyme
UBP8
De-ubiquitylating enzyme that associates with TBP-associated factors in SAGA chromatin-remodelling complex
81
91
82,83
32
14
102
34
CTD, carboxy-terminal domain; pol II, RNA polymerase II; SAGA, Spt–Ada–GCN5–acetyltransferase; TAFII250, TATA-binding protein (TBP)-associated factor 250; TAD,
transcriptional activation domain; TBP, TATA-binding protein; TCR, transcription-coupled repair; TFIID, transcription factor IID; Ub, ubiquitin; UBP8, ubiquitin-specific protease 8.
link between activator destruction and proteasome
involvement in transcription. The relevance of 19S subunits to transcription in vivo was established by the
demonstration that at least five 19S subunits are recruited
to transcriptionally active genes in yeast — in which they
seem to congregate not just at the promoter, but throughout the entire transcribed sequence of the gene29.
The involvement of these proteasomal proteins in
transcription clearly establishes the interconnectivity of
the transcription and Ub–proteasome systems but, like
any interesting observation, it raises more questions
than it answers. How, for example, is the 19S subunit of
the proteasome recruited to an active gene? Is this
recruitment dependent on the ubiquitylation of pol II,
histones or transcriptional activators? Or do proteins
like Med8, which have been found in both the proteasome95 and the pol II holoenzyme96, connect these two
pathways? Similarly, it is unclear whether the 19S subunit is working in isolation or in conjunction with the
entire proteasome. Johnston and colleagues have suggested that a sub-19S complex, known as APIS29, is
required for transcription independent of the 26S complex, but it is, at present, unknown whether there is such
a complex in the cell. And finally, what is the mechanism
through which these 19S subunits stimulate elongation?
Is the proteasome acting as a molecular chaperone, or
are other activities at work? The chaperone-like ATPase
functions of Sug1 and other proteins in the 19S complex
— which, intriguingly, are stimulated by RNA97 — are
ideally suited to orchestrating the rearrangements that
are required for transcription. It is possible that these
chaperone activities facilitate the conversion of pol II to
an elongation-competent form, disengage inhibitor
molecules, stimulate chromatin remodelling, or do all of
the above.
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Although we have focused on the proteasome in
this discussion, there are many other examples of
crosstalk between the transcription and ubiquitylation
machineries (TABLE 1), including a growing number of
Ub-ligase/co-activators, polymerase/proteasomeinteracting factors and even a Ub-ligase that associates
directly with the pol II holoenzyme74. The growing
number of proteins that have double duties in these
two pathways indicates that there is a deeply rooted
mechanistic connection between transcription and the
Ub–proteasome system that we have yet to fully
understand.
A unified model?
From the examples that are discussed in this review, it is
clear that the Ub–proteasome system influences transcription in several diverse ways, which range from the
regulation of chromatin through to the destruction of
transcriptional activators. These disparate functions
indicate a complex, multifaceted role for this system in
gene regulation. Despite the wide-ranging influence of
the Ub–proteasome system on transcription, however, it
is possible to synthesize many of the observations that
we have described into a coherent, but speculative, view
of transcriptional control (FIG. 5).
We propose a model of activation in which activator ubiquitylation, activity and destruction all occur in
a narrow window of space and time. In this model,
components of the Ub–proteasome system converge
on promoters to regulate the activity of numerous
transcriptional components. We imagine that, at some
point during the activation process, transcriptional
activators recruit one or more Ub-ligases to promoter
complexes; this recruitment might be direct, or it
might be mediated by the contact of activators with
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a
b
Activator
Ub
Ub
Ub Ub
Ub-ligase(s)
DNA
pol II
Ub
Ub
Nucleosome
c
Ub
pol II
Ub
Ub
Ub Ub
d
26S proteasome
Ub
Ub
Ub
pol II
pol II
Ub
Ub
RNA
Figure 5 | A unified model? In this model, the ubiquitin (Ub)–proteasome system regulates transcription at numerous levels.
a | Interactions of an activator with the general transcriptional machinery (green) functions to b | recruit ubiquitin ligase(s) to the site of
transcription and ubiquitylates many factors, including the activator, RNA polymerase II (pol II) and histones. c | These ubiquitylation
events in turn recruit the 26S proteasome, which d | simultaneously destroys the activator and promotes elongation of transcription
by pol II. Importantly, this proposed mechanism limits uncontrolled transcription in two ways — by destroying the activator at each
cycle of promoter ‘firing’ and by ensuring that interactions between pol II and the proteasome are made in an activator- and
promoter-dependent manner.
components of the basal transcriptional machinery.
Once recruited, Ub-ligases ubiquitylate their cognate
activators, as well as pol II, histones and possibly
other members of the transcriptional entourage.
Ubiquitylation of the locus then functions to recruit
components of the proteasome. Although it is possible
that the APIS complex first enters the promoter, followed at a later stage by the remainder of the proteasome29, we prefer a more simple model in which the
entire 26S proteasome is recruited to the activated gene
en masse. Recruitment of the 26S proteasome then has
a dual role, both destroying the activator — preventing
reinitiation of transcription — and converting RNA
polymerase from an initiation- to elongation-competent
form that can transcribe the entire gene. As transcription
elongates, the proteasome moves with polymerase,
reconfiguring chromatin structure, and allowing the
disengagement of pol II either at the end of the gene,
or when a damaged DNA segment is detected. Finally,
following gene transcription, the changes in phosphorylation of the CTD cause RNA polymerase and the
proteasome to dissociate, which allows RNA polymerase to assume its initiation-competent form. In
1.
2.
3.
4.
5.
8
Varshavsky, A. The ubiquitin system. Trends Biochem. Sci.
22, 383–387 (1997).
Terrell, J., Shih, S., Dunn, R. & Hicke, L. A function for
monoubiquitination in the internalization of a G proteincoupled receptor. Mol. Cell 1, 193–202 (1998).
Spence, J. et al. Cell cycle-regulated modification of the
ribosome by a variant multiubiquitin chain. Cell 102,
67–76 (2000).
Russell, S. J., Reed, S. H., Huang, W., Friedberg, E. C. &
Johnston, S. A. The 19S regulatory complex of the
proteasome functions independently of proteolysis in
nucleotide excision repair. Mol. Cell 3, 687–695 (1999).
Goldknopf, I. L. et al. Isolation and characterization of
protein A24, a ‘histone-like’ non-histone chromosomal
protein. J. Biol. Chem. 250, 7182–7187 (1975).
6.
7.
8.
9.
this way, the transient activator-induced interaction of
pol II with the proteasome is a self-limiting mechanism that resets the regulatory clock for another
round of gene transcription. Although this model is
probably a gross simplification, it does provide a
framework to build on to understand why the
Ub–proteasome system seems to have invaded so
many aspects of transcriptional control.
Conclusion
In this review, we have tried to give the reader a sense of
the scale on which Ub and its extended family regulates
gene expression. It is worth remembering, in this context, that transcription and the Ub–proteasome system
are two ancient processes that have had a lot of time to
intermingle, and so it seems probable that the full
extent to which these processes are connected has not
yet been revealed. In the future, we can expect many
more surprises as new regulatory strategies are uncovered and — crucially — as the underlying transcriptional mechanisms are understood. And it’s a good bet
that transcription won’t be the only process that is so
heavily managed by the aptly-named ubiquitin system.
Goldknopf, I. L. & Busch, H. Isopeptide linkage between
nonhistone and histone 2A polypeptides of chromosomal
conjugate-protein A24. Proc. Natl Acad. Sci. USA 74,
864–868 (1977).
Hunt, L. T. & Dayhoff, M. O. Amino-terminal sequence
identity of ubiquitin and the nonhistone component of
nuclear protein A24. Biochem. Biophys. Res. Commun. 74,
650–655 (1977).
Levinger, L. & Varshavsky, A. Selective arrangement
of ubiquitinated and D1 protein-containing nucleosomes
within the Drosophila genome. Cell 28, 375–385
(1982).
Nickel, B. E., Allis, C. D. & Davie, J. R. Ubiquitinated histone
H2B is preferentially located in transcriptionally active
chromatin. Biochemistry 28, 958–963 (1989).
| MARCH 2003 | VOLUME 4
10. Davie, J. R. & Murphy, L. C. Level of ubiquitinated histone
H2B in chromatin is coupled to ongoing transcription.
Biochemistry 29, 4752–4757 (1990).
11. Davie, J. R., Lin, R. & Allis, C. D. Timing of the appearance of
ubiquitinated histones in developing new macronuclei of
Tetrahymena thermophila. Biochem. Cell Biol. 69, 66–71 (1991).
12. Vavra, K. J., Allis, C. D. & Gorovsky, M. A. Regulation of
histone acetylation in Tetrahymena macro- and micronuclei.
J. Biol. Chem. 257, 2591–2598 (1982).
13. Huang, S. Y. et al. The active immunoglobulin κ chain gene is
packaged by non-ubiquitin-conjugated nucleosomes. Proc.
Natl Acad. Sci. USA 83, 3738–3742 (1986).
14. Pham, A. D. & Sauer, F. Ubiquitin-activating/conjugating
activity of TAFII250, a mediator of activation of gene
expression in Drosophila. Science 289, 2357–2360 (2000).
www.nature.com/reviews/molcellbio
© 2003 Nature Publishing Group
REVIEWS
15. Chen, H. Y., Sun, J. M., Zhang, Y., Davie, J. R. & Meistrich,
M. L. Ubiquitination of histone H3 in elongating spermatids
of rat testes. J. Biol. Chem. 273, 13165–13169 (1998).
16. Robzyk, K., Recht, J. & Osley, M. A. Rad6-dependent
ubiquitination of histone H2B in yeast. Science 287,
501–504 (2000).
Identified Rad6 as a Ub-conjugating enzyme for
histone H2B in budding yeast and opened the way for
genetic analysis of histone ubiquitylation.
17. Turner, S. D. et al. The E2 ubiquitin conjugase Rad6 is
required for the ArgR/Mcm1 repression of ARG1
transcription. Mol. Cell. Biol. 22, 4011–4019 (2002).
18. Sun, Z. W. & Hampsey, M. A general requirement for the
Sin3-Rpd3 histone deacetylase complex in regulating
silencing in Saccharomyces cerevisiae. Genetics 152,
921–932 (1999).
19. Huang, H., Kahana, A., Gottschling, D. E., Prakash, L. &
Liebman, S. W. The ubiquitin-conjugating enzyme Rad6
(Ubc2) is required for silencing in Saccharomyces cerevisiae.
Mol. Cell. Biol. 17, 6693–6699 (1997).
20. Bryk, M. et al. Transcriptional silencing of Ty1 elements in the
RDN1 locus of yeast. Genes Dev. 11, 255–269 (1997).
21. Ricci, A. R., Genereaux, J. & Brandl, C. J. Components of
the SAGA histone acetyltransferase complex are required
for repressed transcription of ARG1 in rich medium. Mol.
Cell. Biol. 22, 4033–4042 (2002).
22. Sun, Z. W. & Allis, C. D. Ubiquitination of histone H2B
regulates H3 methylation and gene silencing in yeast. Nature
418, 104–108 (2002).
Established that histone ubiquitylation is required for
subsequent histone modifications that are important
in gene silencing.
23. Briggs, S. D. et al. Gene silencing: Trans-histone regulatory
pathway in chromatin. Nature 418, 498 (2002).
24. Rice, J. C. & Allis, C. D. Histone methylation versus histone
acetylation: new insights into epigenetic regulation. Curr.
Opin. Cell Biol. 13, 263–273 (2001).
25. Strahl, B. D. & Allis, C. D. The language of covalent histone
modifications. Nature 403, 41–45 (2000).
26. Seale, R. L. Rapid turnover of the histone-ubiquitin
conjugate, protein A24. Nucleic Acids Res. 9, 3151–3158
(1981).
27. Wu, R. S., Kohn, K. W. & Bonner, W. M. Metabolism of
ubiquitinated histones. J. Biol. Chem. 256, 5916–5920 (1981).
28. Haas, A., Reback, P. M., Pratt, G. & Rechsteiner, M.
Ubiquitin-mediated degradation of histone H3 does not
require the substrate-binding ubiquitin protein ligase, E3, or
attachment of polyubiquitin chains. J. Biol. Chem. 265,
21664–21669 (1990).
29. Gonzalez, F., Delahodde, A., Kodadek, T. & Johnston, S. A.
Recruitment of a 19S proteasome subcomplex to an
activated promoter. Science 296, 548–550 (2002).
Showed that components of the 19S proteasome
are recruited to a transcriptionally-active gene in
yeast.
30. Hook, S. S., Orian, A., Cowley, S. M. & Eisenman, R. N.
Histone deacetylase 6 binds polyubiquitin through its zinc
finger (PAZ domain) and copurifies with deubiquitinating
enzymes. Proc. Natl Acad. Sci. USA 99, 13425–13430
(2002).
31. Santos-Rosa, H. et al. Active genes are tri-methylated at K4
of histone H3. Nature 419, 407–411 (2002).
32. Chen, J. L., Attardi, L. D., Verrijzer, C. P., Yokomori, K. &
Tjian, R. Assembly of recombinant TFIID reveals differential
coactivator requirements for distinct transcriptional
activators. Cell 79, 93–105 (1994).
33. Moazed, D. & Johnson, D. A deubiquitinating enzyme
interacts with SIR4 and regulates silencing in S. cerevisiae.
Cell 86, 667–677 (1996).
34. Sanders, S. L., Garbett, K. A. & Weil, P. A. Molecular
characterization of Saccharomyces cerevisiae TFIID. Mol.
Cell. Biol. 22, 6000–6013 (2002).
35. Svejstrup, J. Q. Mechanisms of transcription-coupled DNA
repair. Nature Rev. Mol. Cell. Biol. 3, 21–29 (2002).
36. Lee, K. B., Wang, D., Lippard, S. J. & Sharp, P. A.
Transcription-coupled and DNA damage-dependent
ubiquitination of RNA polymerase II in vitro. Proc. Natl Acad.
Sci. USA 99, 4239–4244 (2002).
Provided biochemical evidence that DNA-damagedependent ubiquitylation of RNA polymerase II is
coupled to transcription.
37. Beaudenon, S. L., Huacani, M. R., Wang, G., McDonnell, D. P.
& Huibregtse, J. M. Rsp5 ubiquitin-protein ligase mediates
DNA damage-induced degradation of the large subunit of
RNA polymerase II in Saccharomyces cerevisiae. Mol. Cell.
Biol. 19, 6972–6979 (1999).
38. Huibregtse, J. M., Yang, J. C. & Beaudenon, S. L. The large
subunit of RNA polymerase II is a substrate of the Rsp5
ubiquitin-protein ligase. Proc. Natl Acad. Sci. USA 94,
3656–3661 (1997).
39. Komarnitsky, P., Cho, E. J. & Buratowski, S. Different
phosphorylated forms of RNA polymerase II and associated
mRNA processing factors during transcription. Genes Dev.
14, 2452–2460 (2000).
40. Mitsui, A. & Sharp, P. A. Ubiquitination of RNA polymerase II
large subunit signaled by phosphorylation of carboxylterminal domain. Proc. Natl Acad. Sci. USA 96, 6054–6059
(1999).
41. Imhof, M. O. & McDonnell, D. P. Yeast RSP5 and its
human homolog hRPF1 potentiate hormone-dependent
activation of transcription by human progesterone and
glucocorticoid receptors. Mol. Cell. Biol. 16, 2594–2605
(1996).
42. Woudstra, E. C. et al. A Rad26-Def1 complex coordinates
repair and RNA pol II proteolysis in response to DNA
damage. Nature 415, 929–933 (2002).
43. Darnell, J. E., Jr. STATs and gene regulation. Science 277,
1630–1635 (1997).
44. Brown, M. S., Ye, J., Rawson, R. B. & Goldstein, J. L.
Regulated intramembrane proteolysis: a control mechanism
conserved from bacteria to humans. Cell 100, 391–398
(2000).
45. Palombella, V. J., Rando, O. J., Goldberg, A. L. & Maniatis, T.
The ubiquitin-proteasome pathway is required for
processing the NF-κB1 precursor protein and the activation
of NF-κB. Cell 78, 773–785 (1994).
46. Hoppe, T. et al. Activation of a membrane-bound
transcription factor by regulated ubiquitin/proteasomedependent processing. Cell 102, 577–586 (2000).
47. Rape, M. et al. Mobilization of processed, membranetethered SPT23 transcription factor by
CDC48(UFD1/NPL4), a ubiquitin-selective chaperone.
Cell 107, 667–677 (2001).
48. Borden, K. L. Pondering the promyelocytic leukemia protein
(PML) puzzle: possible functions for PML nuclear bodies.
Mol. Cell. Biol. 22, 5259–5269 (2002).
49. Muller, S., Matunis, M. J. & Dejean, A. Conjugation with the
ubiquitin-related modifier SUMO-1 regulates the partitioning
of PML within the nucleus. EMBO J. 17, 61–70 (1998).
50. Sachdev, S. et al. PIASy, a nuclear matrix-associated SUMO
E3 ligase, represses LEF1 activity by sequestration into
nuclear bodies. Genes Dev. 15, 3088-3103 (2001).
Established a solid connection between SUMOmodification of a transcription factor, transcriptional
regulation and PML-body formation.
51. Ross, S., Best, J. L., Zon, L. I. & Gill, G. SUMO-1
modification represses Sp3 transcriptional activation and
modulates its subnuclear localization. Mol. Cell 10, 831–842
(2002).
52. Sapetschnig, A. et al. Transcription factor Sp3 is silenced
through SUMO modification by PIAS1. EMBO J. 21,
5206–5215 (2002).
53. Bies, J., Markus, J. & Wolff, L. Covalent attachment of the
SUMO-1 protein to the negative regulatory domain of the
c-Myb transcription factor modifies its stability and
transactivation capacity. J. Biol. Chem. 277, 8999–9009
(2002).
54. Nishida, T. & Yasuda, H. PIAS1 and PIASxα function as
SUMO-E3 ligases toward androgen receptor and repress
androgen receptor-dependent transcription. J. Biol. Chem.
277, 41311–41317 (2002).
55. Schmidt, D. & Muller, S. Members of the PIAS family act as
SUMO ligases for c-Jun and p53 and repress p53 activity.
Proc. Natl Acad. Sci. USA 99, 2872–2877 (2002).
56. Kim, J., Cantwell, C. A., Johnson, P. F., Pfarr, C. M. &
Williams, S. C. Transcriptional activity of CCAAT/enhancerbinding proteins is controlled by a conserved inhibitory
domain that is a target for sumoylation. J. Biol. Chem. 277,
38037–38044 (2002).
57. Ostendorff, H. P. et al. Ubiquitination-dependent cofactor
exchange on LIM homeodomain transcription factors.
Nature 416, 99–103 (2002).
58. Kaiser, P., Flick, K., Wittenberg, C. & Reed, S. I. Regulation
of transcription by ubiquitination without proteolysis:
Cdc34/SCF(Met30)-mediated inactivation of the
transcription factor Met4. Cell 102, 303–314 (2000).
59. Rouillon, A., Barbey, R., Patton, E. E., Tyers, M. & Thomas, D.
Feedback-regulated degradation of the transcriptional
activator Met4 is triggered by the SCFMet30 complex.
EMBO J. 19, 282–294 (2000).
60. Kuras, L. et al. Dual regulation of the met4 transcription
factor by ubiquitin-dependent degradation and
inhibition of promoter recruitment. Mol. Cell 10, 69–80
(2002).
Showed that the yeast transcription factor
Met4 can be either inactivated or destroyed by
Met30-dependent ubiquitylation, depending on
nutrients.
61. Polakis, P. Wnt signaling and cancer. Genes Dev. 14,
1837–1851 (2000).
NATURE REVIEWS | MOLECUL AR CELL BIOLOGY
62. Aberle, H., Bauer, A., Stappert, J., Kispert, A. & Kemler, R.
β-catenin is a target for the ubiquitin-proteasome pathway.
EMBO J. 16, 3797–3804 (1997).
63. Yost, C. et al. The axis-inducing activity, stability, and
subcellular distribution of β-catenin is regulated in Xenopus
embryos by glycogen synthase kinase 3. Genes Dev. 10,
1443–1454 (1996).
64. Haupt, Y., Maya, R., Kazaz, A. & Oren, M. Mdm2
promotes the rapid degradation of p53. Nature 387,
296–299 (1997).
65. Maxwell, P. H. et al. The tumour suppressor protein VHL
targets hypoxia-inducible factors for oxygen-dependent
proteolysis. Nature 399, 271–275 (1999).
66. Ma, Q. & Baldwin, K. T. 2,3,7,8-tetrachlorodibenzo-p-dioxininduced degradation of aryl hydrocarbon receptor (AhR) by
the ubiquitin-proteasome pathway. Role of the transcription
activation and DNA binding of AhR. J. Biol. Chem. 275,
8432–8438 (2000).
67. Lo, R. S. & Massague, J. Ubiquitin-dependent degradation
of TGF-β-activated Smad2. Nature Cell Biol. 1, 472–478
(1999).
68. Kim, T. K. & Maniatis, T. Regulation of interferon-γ-activated
STAT1 by the ubiquitin-proteasome pathway. Science 273,
1717–1719 (1996).
69. Bertani, D., Oppenheim, A. B. & Narberhaus, F. An internal
region of the RpoH heat shock transcription factor is critical
for rapid degradation by the FtsH protease. FEBS Lett. 493,
17–20 (2001).
70. Becker, G., Klauck, E. & Hengge-Aronis, R. Regulation of
RpoS proteolysis in Escherichia coli: the response regulator
RssB is a recognition factor that interacts with the turnover
element in RpoS. Proc. Natl Acad. Sci. USA 96, 6439–6444
(1999).
71. Salghetti, S. E., Kim, S. Y. & Tansey, W. P. Destruction of
Myc by ubiquitin-mediated proteolysis: cancer-associated
and transforming mutations stabilize Myc. EMBO J. 18,
717–726 (1999).
72. Salghetti, S. E., Muratani, M., Wijnen, H., Futcher, B. &
Tansey, W. P. Functional overlap of sequences that
activate transcription and signal ubiquitin-mediated
proteolysis. Proc. Natl Acad. Sci. USA 97, 3118–3123
(2000).
73. Molinari, E., Gilman, M. & Natesan, S. Proteasomemediated degradation of transcriptional activators correlates
with activation domain potency in vivo. EMBO J. 18,
6439–6447 (1999).
74. Brower, C. S. et al. Mammalian mediator subunit mMED8 is
an Elongin BC-interacting protein that can assemble with
Cul2 and Rbx1 to reconstitute a ubiquitin ligase. Proc. Natl
Acad. Sci. USA 99, 10353-10358 (2002).
Established that Ub-ligase activity is directly
associated with the RNA polymerase II holoenzyme.
75. Chi, Y. et al. Negative regulation of Gcn4 and Msn2
transcription factors by Srb10 cyclin-dependent kinase.
Genes Dev. 15, 1078–1092 (2001).
Showed that the yeast transcription factor GCN4 is
marked for destruction by a kinase that is present in
the RNA polymerase II holoenzyme.
76. Liao, S. M. et al. A kinase-cyclin pair in the RNA polymerase II
holoenzyme. Nature 374, 193–196 (1995).
77. Tansey, W. P. Transcriptional activation: risky business.
Genes Dev. 15, 1045–1050 (2001).
78. Thomas, D. & Tyers, M. Kamikaze activators. Curr. Biol. 10,
R341–R343 (2000).
79. Salghetti, S. E., Caudy, A. A., Chenoweth, J. G. & Tansey, W. P.
Regulation of transcriptional activation domain function by
ubiquitin. Science 293, 1651–1653 (2001).
Showed that ubiquitylation of a transcription factor
bearing the prototypical VP16 activation domain can
be required for transcriptional activation.
80. Xie, Y. & Varshavsky, A. RPN4 is a ligand, substrate, and
transcriptional regulator of the 26S proteasome: a negative
feedback circuit. Proc. Natl Acad. Sci. USA 98, 3056–3061
(2001).
81. Voges, D., Zwickl, P. & Baumeister, W. The 26S
proteasome: a molecular machine designed for
controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068
(1999).
82. Swaffield, J. C., Bromberg, J. F. & Johnston, S. A.
Alterations in a yeast protein resembling HIV Tat-binding
protein relieve requirement for an acidic activation domain in
GAL4. Nature 357, 698–700 (1992).
83. Russell, S. J., Sathyanarayana, U. G. & Johnston, S. A.
Isolation and characterization of SUG2. A novel ATPase
family component of the yeast 26 S proteasome. J. Biol.
Chem. 271, 32810–32817 (1996).
84. Swaffield, J. C., Melcher, K. & Johnston, S. A. A highly
conserved ATPase protein as a mediator between acidic
activation domains and the TATA-binding protein. Nature
374, 88–91 (1995).
VOLUME 4 | MARCH 2003 | 9
© 2003 Nature Publishing Group
REVIEWS
85. Masuyama, H. & MacDonald, P. N. Proteasome-mediated
degradation of the vitamin D receptor (VDR) and a putative
role for SUG1 interaction with the AF-2 domain of VDR.
J. Cell. Biochem. 71, 429–440 (1998).
86. vom Baur, E. et al. Differential ligand-dependent interactions
between the AF-2 activating domain of nuclear receptors
and the putative transcriptional intermediary factors mSUG1
and TIF1. EMBO J. 15, 110–124 (1996).
87. Wang, W., Chevray, P. M. & Nathans, D. Mammalian Sug1
and c-Fos in the nuclear 26S proteasome. Proc. Natl Acad.
Sci. USA 93, 8236–8240 (1996).
88. Melcher, K. & Johnston, S. A. GAL4 interacts with TATA-binding
protein and coactivators. Mol. Cell. Biol. 15, 2839–2848 (1995).
89. Makino, Y. et al. Multiple mammalian proteasomal ATPases,
but not proteasome itself, are associated with TATA-binding
protein and a novel transcriptional activator, TIP120. Genes
Cells 4, 529–539 (1999).
90. Weeda, G. et al. The XPB subunit of repair/transcription
factor TFIIH directly interacts with SUG1, a subunit of the
26S proteasome and putative transcription factor. Nucleic
Acids Res. 25, 2274–2283 (1997).
91. Kim, Y. J., Bjorklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D.
A multiprotein mediator of transcriptional activation and its
interaction with the C-terminal repeat domain of RNA
polymerase II. Cell 77, 599–608 (1994).
92. Russell, S. J. & Johnston, S. A. Evidence that proteolysis of
Gal4 cannot explain the transcriptional effects of
proteasome ATPase mutations. J. Biol. Chem. 276,
9825–9831 (2001).
10
93. Ferdous, A., Gonzalez, F., Sun, L., Kodadek, T. &
Johnston, S. A. The 19S regulatory particle of the
proteasome is required for efficient transcription elongation
by RNA polymerase II. Mol. Cell 7, 981–991 (2001).
94. Blau, J. et al. Three functional classes of transcriptional
activation domain. Mol. Cell. Biol. 16, 2044–2055 (1996).
95. Verma, R. et al. Proteasomal proteomics: identification of
nucleotide-sensitive proteasome-interacting proteins by
mass spectrometric analysis of affinity-purified
proteasomes. Mol. Biol. Cell 11, 3425–3439 (2000).
96. Myers, L. C. et al. The Med proteins of yeast and their
function through the RNA polymerase II carboxy-terminal
domain. Genes Dev. 12, 45–54 (1998).
97. Makino, Y. et al. SUG1, a component of the 26 S
proteasome, is an ATPase stimulated by specific RNAs.
J. Biol. Chem. 272, 23201–23205 (1997).
98. Albert, T. K. et al. Identification of a ubiquitin-protein ligase
subunit within the CCR4-NOT transcription repressor
complex. EMBO J. 21, 355–364 (2002).
99. Aso, T., Lane, W. S., Conaway, J. W. & Conaway, R. C.
Elongin (SIII): a multisubunit regulator of elongation by RNA
polymerase II. Science 269, 1439–1443 (1995).
100. Mueller, C. L. & Jaehning, J. A. Ctr9, Rtf1, and Leo1 are
components of the Paf1/RNA polymerase II complex.
Mol. Cell. Biol. 22, 1971–1980 (2002).
101. Huibregtse, J. M., Scheffner, M., Beaudenon, S. &
Howley, P. M. A family of proteins structurally and
functionally related to the E6-AP ubiquitin-protein ligase.
Proc. Natl Acad. Sci. USA 92, 2563–2567 (1995).
| MARCH 2003 | VOLUME 4
102. Saleh, A. et al. TOM1p, a yeast hect–domain protein
which mediates transcriptional regulation through the
ADA/SAGA coactivator complexes. J. Mol. Biol. 282,
933–946 (1998).
Acknowledgements
We thanks Simone Salghetti for critical comments on the manuscript. W. P. T. is a Leukemia and Lymphoma Society of America
Scholar. M. M. is a Marjorie H. Anderson Fellow. Work in W. P. T.’s
laboratory is supported by a Cold Spring Harbor Laboratory
Cancer Center Support Grant and by a US Public Health Service
Grant from the National Cancer Institute.
Online links
DATABASES
The following terms in this article are linked online to:
Saccharomyces Genome Database:
http://genome-www.stanford.edu/Saccharomyces/
ARG1 | Def1 | Med8
Swiss-Prot: http://www.expasy.ch/
β-catenin | Gal4 | GSK-3β | histone deactylase 6 | Lef1 | Met4 |
Met30 | PIASy | Rad6 | Rad26 | RLIM | Rsp5 | SIR4 | Spt23 |
Srb10 | Sug1 | Sug2 | TAFII250
FURTHER INFORMATION
William P. Tansey’s laboratory: http://tanseylab.cshl.edu
Access to this interactive links box is free online.
www.nature.com/reviews/molcellbio
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